Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbj Working: n-1-17.cluster.ucsf.bkslab.org:/scratch/xiaobo/150923/xbj-8058088.36 Result: /scratch/xiaobo/150923/xbj-8058088.36 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj 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/xab/inputs/xbj mkdir: created directory `/scratch/xiaobo/150923' mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36' /scratch/xiaobo/150923/xbj-8058088.36 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/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/150923/xbj-8058088.36/working' mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/protonate' Storing results in /scratch/xiaobo/150923/xbj-8058088.36/finished Working in /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 /scratch/xiaobo/150923/xbj-8058088.36/working/protonate /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 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/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Bulk generating 3D conformations all protomers in /scratch/xiaobo/150923/xbj-8058088.36/working/3D mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/150923/xbj-8058088.36/working/protonate/xbj-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 ZINC001525309064 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building' mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525309064' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525309064 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001525309064 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525309064/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525309064 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/1 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(Cl)cc1) `ZINC001525309064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525309064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525309064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001525309064 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 18, 18, 18, 18, 18, 5, 10, 10, 9, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 102 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525309064 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525309064 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/finished' Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525309064/0.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525309064 Building ZINC001525358709 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525358709 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/2 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)c1) `ZINC001525358709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525358709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525358709 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 17, 17, 17, 26, 26, 17, 17, 26, 26, 17, 17, 4, 4, 4, 4, 2, 4, 4, 2, 3, 3, 3, 26, 26, 26, 26, 17, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/3 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)c1) `ZINC001525358709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525358709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525358709 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 18, 18, 18, 28, 28, 18, 18, 28, 28, 18, 18, 5, 5, 5, 5, 2, 5, 5, 3, 4, 4, 4, 28, 28, 28, 28, 18, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525358709 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 Building ZINC001525358709 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525358709 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 2) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)c1) `ZINC001525358709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525358709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525358709 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 17, 17, 17, 26, 26, 17, 17, 26, 26, 17, 17, 4, 4, 4, 4, 2, 4, 4, 2, 3, 3, 3, 26, 26, 26, 26, 17, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 3) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)c1) `ZINC001525358709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525358709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525358709 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 18, 18, 18, 28, 28, 18, 18, 28, 28, 18, 18, 5, 5, 5, 5, 2, 5, 5, 3, 4, 4, 4, 28, 28, 28, 28, 18, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525358709 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358709 Building ZINC001525358713 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525358713 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/4 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)c1) `ZINC001525358713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525358713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525358713 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 19, 19, 19, 29, 29, 19, 19, 29, 29, 19, 19, 4, 4, 4, 4, 2, 4, 4, 3, 4, 4, 4, 29, 29, 29, 29, 19, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/5 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)c1) `ZINC001525358713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525358713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525358713 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 17, 17, 17, 25, 25, 17, 25, 25, 25, 17, 17, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 3, 25, 25, 25, 25, 17, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525358713 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 Building ZINC001525358713 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525358713 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 4) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)c1) `ZINC001525358713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525358713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525358713 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 19, 19, 19, 29, 29, 19, 19, 29, 29, 19, 19, 4, 4, 4, 4, 2, 4, 4, 3, 4, 4, 4, 29, 29, 29, 29, 19, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 5) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)c1) `ZINC001525358713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525358713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525358713 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 17, 17, 17, 25, 25, 17, 25, 25, 25, 17, 17, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 3, 25, 25, 25, 25, 17, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525358713 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525358713 Building ZINC001525359805 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525359805 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/6 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c(C)cccc1C) `ZINC001525359805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525359805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001525359805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c(C)cccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/7 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c(C)cccc1C) `ZINC001525359805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525359805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001525359805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c(C)cccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525359805 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 Building ZINC001525359805 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525359805 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 6) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c(C)cccc1C) `ZINC001525359805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525359805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001525359805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c(C)cccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 7) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c(C)cccc1C) `ZINC001525359805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525359805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001525359805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c(C)cccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525359805 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525359805 Building ZINC001525372085 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525372085 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/8 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(C)cc2)cc1Cl) `ZINC001525372085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525372085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525372085 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 5, 10, 10, 10, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 12, 12, 12, 6, 6, 5, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/9 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(C)cc2)cc1Cl) `ZINC001525372085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525372085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525372085 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 4, 9, 9, 9, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 12, 12, 12, 6, 6, 4, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525372085 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 Building ZINC001525372085 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525372085 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 8) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(C)cc2)cc1Cl) `ZINC001525372085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525372085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525372085 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 5, 10, 10, 10, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 12, 12, 12, 6, 6, 5, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 9) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(C)cc2)cc1Cl) `ZINC001525372085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525372085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525372085 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 4, 9, 9, 9, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 12, 12, 12, 6, 6, 4, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525372085 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525372085 Building ZINC001525385851 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525385851 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/10 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/10' -> `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(c2ccc(C(C)C)cc2)nn1c1ccccc1) `ZINC001525385851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525385851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001525385851 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(C(C)C)cc2)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 8, 17, 17, 17, 40, 40, 26, 33, 40, 40, 40, 40, 17, 17, 17, 19, 19, 18, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 18, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/11 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/11' -> `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(c2ccc(C(C)C)cc2)nn1c1ccccc1) `ZINC001525385851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525385851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001525385851 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(C(C)C)cc2)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 9, 18, 18, 18, 41, 41, 24, 27, 42, 42, 41, 41, 18, 18, 18, 20, 20, 19, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 18, 41, 41, 42, 42, 42, 42, 42, 42, 42, 41, 41, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 203 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525385851 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 Building ZINC001525385851 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525385851 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 10) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(C(C)C)cc2)nn1c1ccccc1) `ZINC001525385851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525385851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001525385851 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(C(C)C)cc2)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 8, 17, 17, 17, 40, 40, 26, 33, 40, 40, 40, 40, 17, 17, 17, 19, 19, 18, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 18, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 11) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(C(C)C)cc2)nn1c1ccccc1) `ZINC001525385851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525385851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001525385851 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(C(C)C)cc2)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 9, 18, 18, 18, 41, 41, 24, 27, 42, 42, 41, 41, 18, 18, 18, 20, 20, 19, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 18, 41, 41, 42, 42, 42, 42, 42, 42, 42, 41, 41, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 203 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525385851 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385851 Building ZINC001525385964 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525385964 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/12 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n(c3ccccc3)n2)c1) `ZINC001525385964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525385964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001525385964 none Cc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n(c3ccccc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 8, 34, 34, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 34, 34, 34, 4, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 4, 4, 4, 4, 4, 34] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/13 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n(c3ccccc3)n2)c1) `ZINC001525385964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525385964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001525385964 none Cc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n(c3ccccc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 4, 33, 33, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 4, 33, 33, 4, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 4, 4, 4, 4, 4, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525385964 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 Building ZINC001525385964 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525385964 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 12) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n(c3ccccc3)n2)c1) `ZINC001525385964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525385964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001525385964 none Cc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n(c3ccccc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 8, 34, 34, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 34, 34, 34, 4, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 4, 4, 4, 4, 4, 34] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 13) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n(c3ccccc3)n2)c1) `ZINC001525385964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525385964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001525385964 none Cc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n(c3ccccc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 4, 33, 33, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 4, 33, 33, 4, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 4, 4, 4, 4, 4, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525385964 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525385964 Building ZINC001525387140 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525387140 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/14 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccccc2C)cc1Cl) `ZINC001525387140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525387140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525387140 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccccc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 14, 14, 14, 8, 8, 8, 15, 15, 8, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 8, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/15 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccccc2C)cc1Cl) `ZINC001525387140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525387140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525387140 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccccc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 15, 15, 15, 8, 8, 8, 15, 15, 12, 15, 14, 15, 6, 6, 6, 10, 10, 10, 6, 6, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525387140 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 Building ZINC001525387140 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525387140 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 14) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccccc2C)cc1Cl) `ZINC001525387140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525387140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525387140 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccccc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 14, 14, 14, 8, 8, 8, 15, 15, 8, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 8, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 15) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccccc2C)cc1Cl) `ZINC001525387140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525387140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525387140 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccccc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 15, 15, 15, 8, 8, 8, 15, 15, 12, 15, 14, 15, 6, 6, 6, 10, 10, 10, 6, 6, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525387140 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525387140 Building ZINC001525401028 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525401028 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/16 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(COCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525401028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525401028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525401028 none O=C(NCc1cccc(COCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 13, 13, 8, 13, 13, 19, 20, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 13, 13, 9, 19, 19, 50, 50, 50, 50, 50, 50, 50, 13, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/17 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(COCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525401028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525401028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525401028 none O=C(NCc1cccc(COCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 13, 13, 13, 13, 13, 19, 20, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 13, 13, 13, 19, 19, 50, 50, 50, 50, 50, 50, 50, 13, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525401028 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 Building ZINC001525401028 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525401028 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 16) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(COCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525401028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525401028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525401028 none O=C(NCc1cccc(COCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 13, 13, 8, 13, 13, 19, 20, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 13, 13, 9, 19, 19, 50, 50, 50, 50, 50, 50, 50, 13, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 17) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(COCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525401028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525401028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525401028 none O=C(NCc1cccc(COCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 13, 13, 13, 13, 13, 19, 20, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 13, 13, 13, 19, 19, 50, 50, 50, 50, 50, 50, 50, 13, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525401028 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525401028 Building ZINC001525416214 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525416214 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/18 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cc(C)ccc21) `ZINC001525416214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525416214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525416214 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cc(C)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 4, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 10, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/19 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cc(C)ccc21) `ZINC001525416214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525416214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525416214 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cc(C)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525416214 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 Building ZINC001525416214 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525416214 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 18) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cc(C)ccc21) `ZINC001525416214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525416214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525416214 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cc(C)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 4, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 10, 22, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 19) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cc(C)ccc21) `ZINC001525416214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525416214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525416214 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cc(C)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525416214 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525416214 Building ZINC001525455575 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525455575 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/20 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2ccc(Cl)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001525455575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525455575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525455575 none CC1(c2ccc(Cl)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', '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, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 16, 17, 27, 27, 16, 16, 9, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 27, 27, 27, 27, 16, 16, 16, 16, 10, 10, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/21 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2ccc(Cl)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001525455575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525455575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525455575 none CC1(c2ccc(Cl)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', '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, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 28, 28, 14, 15, 28, 28, 14, 14, 8, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 10, 10, 14, 14, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525455575 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 Building ZINC001525455575 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525455575 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 20) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Cl)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001525455575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525455575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525455575 none CC1(c2ccc(Cl)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', '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, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 16, 17, 27, 27, 16, 16, 9, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 27, 27, 27, 27, 16, 16, 16, 16, 10, 10, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 21) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Cl)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001525455575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525455575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525455575 none CC1(c2ccc(Cl)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', '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, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 28, 28, 14, 15, 28, 28, 14, 14, 8, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 10, 10, 14, 14, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525455575 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455575 Building ZINC001525455934 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525455934 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/22 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCCF)c1) `ZINC001525455934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525455934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525455934 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCCF)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 11, 12, 14, 5, 2, 2, 2, 8, 8, 5, 8, 2, 2, 2, 2, 5, 5, 5, 12, 12, 14, 14, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/23 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OCCF)c1) `ZINC001525455934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525455934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525455934 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OCCF)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 12, 13, 15, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 6, 13, 13, 15, 15, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525455934 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 Building ZINC001525455934 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525455934 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 22) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCCF)c1) `ZINC001525455934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525455934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525455934 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCCF)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 11, 12, 14, 5, 2, 2, 2, 8, 8, 5, 8, 2, 2, 2, 2, 5, 5, 5, 12, 12, 14, 14, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 23) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OCCF)c1) `ZINC001525455934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525455934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525455934 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OCCF)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 12, 13, 15, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 6, 13, 13, 15, 15, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525455934 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525455934 Building ZINC001525459634 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525459634 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/24 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@@H](C)C3)cc1Cl) `ZINC001525459634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525459634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525459634 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@@H](C)C3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 10, 6, 6, 6, 13, 13, 15, 16, 16, 10, 10, 10, 10, 10, 10, 6, 6, 6, 12, 12, 12, 6, 6, 4, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/25 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@@H](C)C3)cc1Cl) `ZINC001525459634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525459634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525459634 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@@H](C)C3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 10, 6, 6, 6, 13, 13, 17, 18, 18, 10, 10, 10, 10, 10, 10, 6, 6, 6, 10, 10, 10, 6, 6, 4, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525459634 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 Building ZINC001525459634 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525459634 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 24) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@@H](C)C3)cc1Cl) `ZINC001525459634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525459634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525459634 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@@H](C)C3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 10, 6, 6, 6, 13, 13, 15, 16, 16, 10, 10, 10, 10, 10, 10, 6, 6, 6, 12, 12, 12, 6, 6, 4, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 25) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@@H](C)C3)cc1Cl) `ZINC001525459634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525459634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525459634 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@@H](C)C3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 10, 6, 6, 6, 13, 13, 17, 18, 18, 10, 10, 10, 10, 10, 10, 6, 6, 6, 10, 10, 10, 6, 6, 4, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525459634 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459634 Building ZINC001525459635 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525459635 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/26 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@H](C)C3)cc1Cl) `ZINC001525459635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525459635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525459635 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@H](C)C3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 10, 10, 6, 10, 21, 21, 24, 27, 27, 10, 10, 10, 10, 10, 10, 6, 6, 6, 11, 11, 11, 6, 6, 4, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/27 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@H](C)C3)cc1Cl) `ZINC001525459635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525459635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525459635 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@H](C)C3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 10, 10, 6, 10, 19, 19, 22, 23, 23, 10, 10, 10, 10, 10, 10, 6, 6, 6, 11, 11, 11, 6, 6, 4, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525459635 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 Building ZINC001525459635 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525459635 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 26) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@H](C)C3)cc1Cl) `ZINC001525459635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525459635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525459635 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@H](C)C3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 10, 10, 6, 10, 21, 21, 24, 27, 27, 10, 10, 10, 10, 10, 10, 6, 6, 6, 11, 11, 11, 6, 6, 4, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 27) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@H](C)C3)cc1Cl) `ZINC001525459635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525459635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001525459635 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)OC(C)C)CC[C@H](C)C3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 10, 10, 6, 10, 19, 19, 22, 23, 23, 10, 10, 10, 10, 10, 10, 6, 6, 6, 11, 11, 11, 6, 6, 4, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525459635 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525459635 Building ZINC001525461548 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525461548 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/28 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccc(Cl)cc2F)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525461548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525461548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001525461548 none O=C(Nc1nnc(c2ccc(Cl)cc2F)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 29, 29, 18, 29, 29, 29, 29, 4, 1, 1, 1, 8, 8, 8, 8, 8, 2, 29, 29, 29, 8, 8] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/29 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccc(Cl)cc2F)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525461548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525461548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001525461548 none O=C(Nc1nnc(c2ccc(Cl)cc2F)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 29, 29, 18, 29, 29, 29, 29, 4, 1, 1, 1, 8, 8, 8, 8, 8, 2, 29, 29, 29, 8, 8] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525461548 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 Building ZINC001525461548 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525461548 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 28) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccc(Cl)cc2F)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525461548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525461548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001525461548 none O=C(Nc1nnc(c2ccc(Cl)cc2F)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 29, 29, 18, 29, 29, 29, 29, 4, 1, 1, 1, 8, 8, 8, 8, 8, 2, 29, 29, 29, 8, 8] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 29) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccc(Cl)cc2F)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525461548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525461548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001525461548 none O=C(Nc1nnc(c2ccc(Cl)cc2F)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 29, 29, 18, 29, 29, 29, 29, 4, 1, 1, 1, 8, 8, 8, 8, 8, 2, 29, 29, 29, 8, 8] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525461548 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525461548 Building ZINC001525490826 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525490826 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/30 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)n(c2ccc(C)cc2)n1) `ZINC001525490826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525490826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001525490826 none COc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)n(c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 44, 10, 44, 44, 7, 7, 7, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 44, 44, 44, 44, 7, 5, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/31 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)n(c2ccc(C)cc2)n1) `ZINC001525490826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525490826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001525490826 none COc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)n(c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 45, 24, 45, 45, 8, 8, 8, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 45, 45, 45, 45, 8, 5, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525490826 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 Building ZINC001525490826 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525490826 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 30) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)n(c2ccc(C)cc2)n1) `ZINC001525490826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525490826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001525490826 none COc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)n(c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 44, 10, 44, 44, 7, 7, 7, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 44, 44, 44, 44, 7, 5, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 31) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)n(c2ccc(C)cc2)n1) `ZINC001525490826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525490826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001525490826 none COc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)n(c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 45, 24, 45, 45, 8, 8, 8, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 45, 45, 45, 45, 8, 5, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525490826 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525490826 Building ZINC001525492697 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525492697 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/32 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001525492697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525492697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525492697 none COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 13, 24, 13, 13, 13, 13, 13, 21, 21, 19, 19, 21, 21, 4, 4, 1, 4, 1, 1, 1, 5, 5, 2, 5, 12, 5, 5, 5, 24, 24, 24, 13, 21, 21, 21, 21, 21, 21, 21, 4, 5, 5, 12, 12, 12, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/33 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001525492697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525492697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525492697 none COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 21, 12, 12, 12, 12, 12, 19, 19, 14, 12, 19, 19, 4, 4, 1, 4, 1, 1, 1, 5, 5, 2, 5, 11, 5, 5, 5, 21, 21, 21, 12, 19, 19, 19, 19, 19, 19, 19, 4, 5, 5, 11, 11, 11, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525492697 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 Building ZINC001525492697 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525492697 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 32) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1scc(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001525492697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525492697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525492697 none COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 13, 24, 13, 13, 13, 13, 13, 21, 21, 19, 19, 21, 21, 4, 4, 1, 4, 1, 1, 1, 5, 5, 2, 5, 12, 5, 5, 5, 24, 24, 24, 13, 21, 21, 21, 21, 21, 21, 21, 4, 5, 5, 12, 12, 12, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 33) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1scc(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001525492697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525492697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525492697 none COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 21, 12, 12, 12, 12, 12, 19, 19, 14, 12, 19, 19, 4, 4, 1, 4, 1, 1, 1, 5, 5, 2, 5, 11, 5, 5, 5, 21, 21, 21, 12, 19, 19, 19, 19, 19, 19, 19, 4, 5, 5, 11, 11, 11, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525492697 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525492697 Building ZINC001525496858 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525496858 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/34 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)n(c3ccc(C)cc3)n2)c1) `ZINC001525496858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525496858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525496858 none COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 46, 46, 8, 8, 8, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 46, 50, 50, 50, 46, 46, 46, 8, 4, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 46] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/35 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)n(c3ccc(C)cc3)n2)c1) `ZINC001525496858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525496858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525496858 none COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 46, 46, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 46, 50, 50, 50, 46, 46, 46, 7, 4, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 46] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525496858 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 Building ZINC001525496858 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525496858 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 34) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)n(c3ccc(C)cc3)n2)c1) `ZINC001525496858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525496858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525496858 none COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 46, 46, 8, 8, 8, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 46, 50, 50, 50, 46, 46, 46, 8, 4, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 46] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 35) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)n(c3ccc(C)cc3)n2)c1) `ZINC001525496858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525496858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525496858 none COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 46, 46, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 46, 50, 50, 50, 46, 46, 46, 7, 4, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 46] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525496858 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525496858 Building ZINC001525497110 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525497110 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/36 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn(Cc2ccccc2)nc1c1ccccc1) `ZINC001525497110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525497110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525497110 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn(Cc2ccccc2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 3, 17, 17, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/37 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1cn(Cc2ccccc2)nc1c1ccccc1) `ZINC001525497110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525497110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525497110 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1cn(Cc2ccccc2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 33, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 3, 17, 17, 33, 50, 50, 50, 50, 50, 50, 50, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525497110 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 Building ZINC001525497110 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525497110 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 36) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn(Cc2ccccc2)nc1c1ccccc1) `ZINC001525497110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525497110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525497110 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn(Cc2ccccc2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 3, 17, 17, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 37) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1cn(Cc2ccccc2)nc1c1ccccc1) `ZINC001525497110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525497110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525497110 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1cn(Cc2ccccc2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 33, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 3, 17, 17, 33, 50, 50, 50, 50, 50, 50, 50, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525497110 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497110 Building ZINC001525497589 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525497589 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/38 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525497589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525497589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525497589 none C[C@@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 19, 19, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 6, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 28, 28, 32, 32, 32, 32, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/39 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525497589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525497589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525497589 none C[C@@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 15, 15, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 3, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 24, 24, 30, 30, 30, 30, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 122 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525497589 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 Building ZINC001525497589 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525497589 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 38) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525497589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525497589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525497589 none C[C@@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 19, 19, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 6, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 28, 28, 32, 32, 32, 32, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 39) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525497589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525497589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525497589 none C[C@@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 15, 15, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 3, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 24, 24, 30, 30, 30, 30, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 122 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525497589 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497589 Building ZINC001525497590 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525497590 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/40 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525497590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525497590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525497590 none C[C@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 16, 16, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 6, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 24, 24, 31, 31, 31, 31, 6, 6, 6, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/41 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525497590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525497590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525497590 none C[C@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 17, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 28, 28, 32, 32, 32, 32, 6, 6, 6, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525497590 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 Building ZINC001525497590 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525497590 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 40) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525497590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525497590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525497590 none C[C@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 16, 16, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 6, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 24, 24, 31, 31, 31, 31, 6, 6, 6, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 41) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525497590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525497590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525497590 none C[C@H](Cc1ccccc1C(F)(F)F)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 17, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 28, 28, 32, 32, 32, 32, 6, 6, 6, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525497590 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525497590 Building ZINC001525513545 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525513545 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/42 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1) `ZINC001525513545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525513545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525513545 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 27, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 31, 38, 38, 31, 38, 38, 38, 31, 31, 31, 31, 31, 31, 13, 13, 2, 7, 7, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/43 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1) `ZINC001525513545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525513545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525513545 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 27, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 31, 38, 38, 33, 38, 38, 38, 31, 31, 31, 31, 31, 31, 13, 13, 2, 7, 7, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525513545 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 Building ZINC001525513545 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525513545 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 42) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1) `ZINC001525513545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525513545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525513545 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 27, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 31, 38, 38, 31, 38, 38, 38, 31, 31, 31, 31, 31, 31, 13, 13, 2, 7, 7, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 43) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1) `ZINC001525513545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525513545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525513545 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 27, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 31, 38, 38, 33, 38, 38, 38, 31, 31, 31, 31, 31, 31, 13, 13, 2, 7, 7, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525513545 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525513545 Building ZINC001525522606 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525522606 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/44 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cccc(F)c1)c1cccc(Br)c1) `ZINC001525522606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525522606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525522606 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cccc(F)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 23, 23, 23, 23, 23, 23, 6, 25, 25, 16, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 25, 25, 17, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/45 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cccc(F)c1)c1cccc(Br)c1) `ZINC001525522606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525522606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525522606 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cccc(F)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 24, 24, 24, 24, 24, 24, 6, 25, 25, 16, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 3, 24, 24, 24, 24, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525522606 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 Building ZINC001525522606 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525522606 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 44) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cccc(F)c1)c1cccc(Br)c1) `ZINC001525522606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525522606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525522606 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cccc(F)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 23, 23, 23, 23, 23, 23, 6, 25, 25, 16, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 25, 25, 17, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 45) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cccc(F)c1)c1cccc(Br)c1) `ZINC001525522606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525522606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525522606 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cccc(F)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 24, 24, 24, 24, 24, 24, 6, 25, 25, 16, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 3, 24, 24, 24, 24, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525522606 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522606 Building ZINC001525522607 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525522607 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/46 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(F)c1)c1cccc(Br)c1) `ZINC001525522607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525522607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525522607 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(F)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 24, 24, 24, 24, 24, 24, 6, 25, 25, 16, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 3, 24, 24, 24, 24, 25, 25, 22, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/47 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(F)c1)c1cccc(Br)c1) `ZINC001525522607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525522607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525522607 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(F)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 23, 23, 23, 23, 23, 23, 6, 25, 25, 16, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525522607 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 Building ZINC001525522607 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525522607 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 46) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(F)c1)c1cccc(Br)c1) `ZINC001525522607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525522607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525522607 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(F)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 24, 24, 24, 24, 24, 24, 6, 25, 25, 16, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 3, 24, 24, 24, 24, 25, 25, 22, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 47) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(F)c1)c1cccc(Br)c1) `ZINC001525522607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525522607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525522607 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(F)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 23, 23, 23, 23, 23, 23, 6, 25, 25, 16, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525522607 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525522607 Building ZINC001525548171 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525548171 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/48 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1) `ZINC001525548171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525548171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525548171 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 27, 46, 46, 46, 46, 46, 7, 7, 5, 5, 5, 3, 5, 5, 7, 7, 46, 46, 46, 46, 7, 7] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/49 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1) `ZINC001525548171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525548171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525548171 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 8, 8, 6, 8, 26, 45, 45, 45, 45, 45, 8, 8, 6, 6, 6, 3, 4, 4, 8, 8, 45, 45, 45, 45, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525548171 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 Building ZINC001525548171 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525548171 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 48) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1) `ZINC001525548171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525548171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525548171 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 27, 46, 46, 46, 46, 46, 7, 7, 5, 5, 5, 3, 5, 5, 7, 7, 46, 46, 46, 46, 7, 7] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 49) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1) `ZINC001525548171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525548171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525548171 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 8, 8, 6, 8, 26, 45, 45, 45, 45, 45, 8, 8, 6, 6, 6, 3, 4, 4, 8, 8, 45, 45, 45, 45, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525548171 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548171 Building ZINC001525548172 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525548172 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/50 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1) `ZINC001525548172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525548172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525548172 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 8, 8, 6, 6, 26, 45, 45, 45, 45, 45, 8, 8, 6, 6, 6, 3, 4, 4, 8, 8, 45, 45, 45, 45, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/51 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1) `ZINC001525548172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525548172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525548172 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 5, 5, 27, 45, 45, 45, 45, 45, 7, 7, 5, 5, 5, 3, 5, 5, 7, 7, 45, 45, 45, 45, 7, 7] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525548172 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 Building ZINC001525548172 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525548172 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 50) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1) `ZINC001525548172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525548172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525548172 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 8, 8, 6, 6, 26, 45, 45, 45, 45, 45, 8, 8, 6, 6, 6, 3, 4, 4, 8, 8, 45, 45, 45, 45, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 51) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1) `ZINC001525548172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525548172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525548172 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Oc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 5, 5, 27, 45, 45, 45, 45, 45, 7, 7, 5, 5, 5, 3, 5, 5, 7, 7, 45, 45, 45, 45, 7, 7] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525548172 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525548172 Building ZINC001525558200 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525558200 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/52 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2nc3ccccc3s2)n1) `ZINC001525558200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525558200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525558200 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 12, 5, 1, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 22, 41, 41, 41, 41, 41, 41, 41, 41, 23, 23, 23, 23, 23, 12, 3, 1, 3, 41, 41, 41, 41] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/53 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2nc3ccccc3s2)n1) `ZINC001525558200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525558200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525558200 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 12, 5, 1, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 42, 42, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 12, 3, 1, 3, 42, 42, 42, 42] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525558200 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 Building ZINC001525558200 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525558200 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 52) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2nc3ccccc3s2)n1) `ZINC001525558200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525558200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525558200 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 12, 5, 1, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 22, 41, 41, 41, 41, 41, 41, 41, 41, 23, 23, 23, 23, 23, 12, 3, 1, 3, 41, 41, 41, 41] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 53) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2nc3ccccc3s2)n1) `ZINC001525558200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525558200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001525558200 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 12, 5, 1, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 42, 42, 42, 42, 42, 42, 42, 42, 22, 22, 22, 22, 22, 12, 3, 1, 3, 42, 42, 42, 42] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525558200 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525558200 Building ZINC001525572987 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525572987 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/54 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001525572987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525572987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525572987 none CCOc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [18, 13, 9, 9, 9, 9, 6, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 18, 18, 18, 18, 18, 9, 9, 3, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/55 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001525572987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525572987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525572987 none CCOc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [18, 13, 9, 9, 9, 9, 6, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 18, 18, 18, 18, 18, 9, 9, 3, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525572987 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 Building ZINC001525572987 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525572987 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 54) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001525572987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525572987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525572987 none CCOc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [18, 13, 9, 9, 9, 9, 6, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 18, 18, 18, 18, 18, 9, 9, 3, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 55) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001525572987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525572987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525572987 none CCOc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [18, 13, 9, 9, 9, 9, 6, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 18, 18, 18, 18, 18, 9, 9, 3, 6, 6, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525572987 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525572987 Building ZINC001525578610 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525578610 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/56 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc(Br)cn2)cs1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001525578610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525578610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001525578610 none O=C(Nc1nc(c2ccc(Br)cn2)cs1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 1, 1, 1, 12, 12, 12, 12, 12, 7, 26, 26, 26, 13, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/57 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc(Br)cn2)cs1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001525578610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525578610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001525578610 none O=C(Nc1nc(c2ccc(Br)cn2)cs1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 1, 1, 1, 12, 12, 12, 12, 12, 7, 26, 26, 26, 13, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525578610 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 Building ZINC001525578610 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525578610 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 56) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc(Br)cn2)cs1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001525578610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525578610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001525578610 none O=C(Nc1nc(c2ccc(Br)cn2)cs1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 1, 1, 1, 12, 12, 12, 12, 12, 7, 26, 26, 26, 13, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 57) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc(Br)cn2)cs1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001525578610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525578610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001525578610 none O=C(Nc1nc(c2ccc(Br)cn2)cs1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 1, 1, 1, 12, 12, 12, 12, 12, 7, 26, 26, 26, 13, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525578610 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525578610 Building ZINC001525590137 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525590137 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/58 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3ccc(Br)cc3)c2)cn1) `ZINC001525590137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525590137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001525590137 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3ccc(Br)cc3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 19, 19, 11, 11, 19, 19, 11, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 11, 11, 11, 19, 19, 19, 19, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/59 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3ccc(Br)cc3)c2)cn1) `ZINC001525590137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525590137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001525590137 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3ccc(Br)cc3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 19, 19, 11, 11, 19, 19, 11, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 11, 11, 11, 19, 19, 19, 19, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525590137 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 Building ZINC001525590137 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525590137 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 58) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3ccc(Br)cc3)c2)cn1) `ZINC001525590137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525590137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001525590137 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3ccc(Br)cc3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 19, 19, 11, 11, 19, 19, 11, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 11, 11, 11, 19, 19, 19, 19, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 59) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3ccc(Br)cc3)c2)cn1) `ZINC001525590137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525590137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001525590137 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3ccc(Br)cc3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 19, 19, 11, 11, 19, 19, 11, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 11, 11, 11, 19, 19, 19, 19, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525590137 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525590137 Building ZINC001525601876 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525601876 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/60 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F) `ZINC001525601876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525601876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525601876 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F 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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 10, 10, 10, 10, 7, 7, 7, 7, 7, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 10, 10] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/61 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F) `ZINC001525601876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525601876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525601876 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F 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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 12, 12, 12, 12, 8, 8, 8, 8, 8, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 12, 12] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525601876 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 Building ZINC001525601876 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525601876 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 60) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F) `ZINC001525601876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525601876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525601876 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F 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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 10, 10, 10, 10, 7, 7, 7, 7, 7, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 10, 10] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 61) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F) `ZINC001525601876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525601876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525601876 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F 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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 12, 12, 12, 12, 8, 8, 8, 8, 8, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 12, 12] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525601876 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601876 Building ZINC001525601877 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525601877 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/62 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F) `ZINC001525601877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525601877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525601877 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F 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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 13, 13, 13, 13, 8, 9, 9, 9, 9, 6, 6, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 13, 13] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/63 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F) `ZINC001525601877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525601877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525601877 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F 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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 10, 10, 10, 10, 7, 7, 7, 7, 7, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 10, 10] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525601877 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 Building ZINC001525601877 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525601877 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 62) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F) `ZINC001525601877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525601877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525601877 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F 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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 13, 13, 13, 13, 8, 9, 9, 9, 9, 6, 6, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 13, 13] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 63) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F) `ZINC001525601877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525601877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525601877 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)CC(F)(F)F 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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 10, 10, 10, 10, 7, 7, 7, 7, 7, 5, 5, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 10, 10] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525601877 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525601877 Building ZINC001525617519 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525617519 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/64 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1ccccc1)C2) `ZINC001525617519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525617519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001525617519 none COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1ccccc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 6, 9, 9, 6, 9, 9, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/65 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1ccccc1)C2) `ZINC001525617519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525617519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001525617519 none COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1ccccc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 8, 8, 8, 10, 10, 8, 10, 10, 8, 13, 13, 13, 8, 8, 8, 8, 8, 6, 6, 11, 11, 11, 6, 10, 10, 8, 10, 10, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525617519 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 Building ZINC001525617519 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525617519 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 64) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1ccccc1)C2) `ZINC001525617519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525617519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001525617519 none COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1ccccc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 6, 9, 9, 6, 9, 9, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 65) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1ccccc1)C2) `ZINC001525617519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525617519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001525617519 none COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1ccccc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 8, 8, 8, 10, 10, 8, 10, 10, 8, 13, 13, 13, 8, 8, 8, 8, 8, 6, 6, 11, 11, 11, 6, 10, 10, 8, 10, 10, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525617519 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617519 Building ZINC001525617520 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525617520 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/66 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1ccccc1)C2) `ZINC001525617520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525617520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001525617520 none COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1ccccc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 5, 5, 2, 5, 9, 5, 5, 5, 10, 10, 10, 15, 15, 12, 15, 15, 10, 17, 17, 17, 10, 10, 10, 10, 10, 5, 5, 9, 9, 9, 5, 15, 15, 14, 15, 15, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/67 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1ccccc1)C2) `ZINC001525617520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525617520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001525617520 none COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1ccccc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 8, 8, 8, 12, 12, 11, 12, 12, 8, 14, 14, 14, 8, 8, 8, 8, 8, 6, 6, 12, 12, 12, 6, 12, 12, 10, 12, 12, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525617520 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 Building ZINC001525617520 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525617520 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 66) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1ccccc1)C2) `ZINC001525617520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525617520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001525617520 none COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1ccccc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 5, 5, 2, 5, 9, 5, 5, 5, 10, 10, 10, 15, 15, 12, 15, 15, 10, 17, 17, 17, 10, 10, 10, 10, 10, 5, 5, 9, 9, 9, 5, 15, 15, 14, 15, 15, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 67) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1ccccc1)C2) `ZINC001525617520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525617520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001525617520 none COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1ccccc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 8, 8, 8, 12, 12, 11, 12, 12, 8, 14, 14, 14, 8, 8, 8, 8, 8, 6, 6, 12, 12, 12, 6, 12, 12, 10, 12, 12, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525617520 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525617520 Building ZINC001525636401 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525636401 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/68 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](OCC1CC1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525636401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525636401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525636401 none O=C(NC[C@H](OCC1CC1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 13, 13, 19, 30, 43, 43, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 4, 9, 9, 30, 30, 43, 43, 43, 43, 43, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/69 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](OCC1CC1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525636401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525636401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525636401 none O=C(NC[C@H](OCC1CC1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 12, 12, 18, 29, 44, 44, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 7, 7, 7, 7, 7, 3, 8, 8, 29, 29, 44, 44, 44, 44, 44, 12, 12, 12, 12, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525636401 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 Building ZINC001525636401 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525636401 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 68) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](OCC1CC1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525636401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525636401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525636401 none O=C(NC[C@H](OCC1CC1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 13, 13, 19, 30, 43, 43, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 4, 9, 9, 30, 30, 43, 43, 43, 43, 43, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 69) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](OCC1CC1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525636401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525636401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525636401 none O=C(NC[C@H](OCC1CC1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 12, 12, 18, 29, 44, 44, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 7, 7, 7, 7, 7, 3, 8, 8, 29, 29, 44, 44, 44, 44, 44, 12, 12, 12, 12, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525636401 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636401 Building ZINC001525636402 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525636402 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/70 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](OCC1CC1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525636402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525636402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525636402 none O=C(NC[C@@H](OCC1CC1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 12, 12, 18, 26, 47, 47, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 7, 7, 7, 7, 7, 3, 8, 8, 26, 26, 47, 47, 47, 47, 47, 12, 12, 12, 12, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/71 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](OCC1CC1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525636402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525636402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525636402 none O=C(NC[C@@H](OCC1CC1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 13, 13, 18, 28, 44, 44, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 7, 7, 7, 7, 7, 4, 9, 9, 28, 28, 44, 44, 44, 44, 44, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525636402 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 Building ZINC001525636402 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525636402 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 70) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](OCC1CC1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525636402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525636402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525636402 none O=C(NC[C@@H](OCC1CC1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 12, 12, 18, 26, 47, 47, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 7, 7, 7, 7, 7, 3, 8, 8, 26, 26, 47, 47, 47, 47, 47, 12, 12, 12, 12, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 71) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](OCC1CC1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525636402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525636402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525636402 none O=C(NC[C@@H](OCC1CC1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 13, 13, 18, 28, 44, 44, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 7, 7, 7, 7, 7, 4, 9, 9, 28, 28, 44, 44, 44, 44, 44, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525636402 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525636402 Building ZINC001525640761 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525640761 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/72 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/72' -> `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)N1CCSc2ccc(C(F)(F)F)cc21) `ZINC001525640761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525640761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525640761 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSc2ccc(C(F)(F)F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 3, 8, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 13, 13, 6, 13, 13, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/73 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/73' -> `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)N1CCSc2ccc(C(F)(F)F)cc21) `ZINC001525640761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525640761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525640761 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSc2ccc(C(F)(F)F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 3, 8, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525640761 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 Building ZINC001525640761 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525640761 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 72) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCSc2ccc(C(F)(F)F)cc21) `ZINC001525640761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525640761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525640761 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCSc2ccc(C(F)(F)F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 3, 8, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 13, 13, 6, 13, 13, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 73) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCSc2ccc(C(F)(F)F)cc21) `ZINC001525640761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525640761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525640761 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCSc2ccc(C(F)(F)F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 3, 8, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525640761 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525640761 Building ZINC001525649020 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525649020 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/74 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525649020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525649020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525649020 none O=C(N[C@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 12, 12, 12, 12, 12, 48, 48, 48, 48, 12, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/75 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525649020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525649020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525649020 none O=C(N[C@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 12, 12, 12, 12, 12, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 2, 12, 12, 12, 12, 4, 4, 4, 4, 4, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525649020 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 Building ZINC001525649020 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525649020 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 74) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525649020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525649020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525649020 none O=C(N[C@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 12, 12, 12, 12, 12, 48, 48, 48, 48, 12, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 75) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525649020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525649020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525649020 none O=C(N[C@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 12, 12, 12, 12, 12, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 2, 12, 12, 12, 12, 4, 4, 4, 4, 4, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525649020 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649020 Building ZINC001525649021 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525649021 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/76 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525649021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525649021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525649021 none O=C(N[C@@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 13, 13, 13, 13, 13, 50, 50, 50, 50, 13, 4, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 6, 6, 6, 6, 6, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/77 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525649021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525649021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525649021 none O=C(N[C@@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 11, 11, 11, 11, 11, 44, 44, 44, 44, 11, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525649021 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 Building ZINC001525649021 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525649021 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 76) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525649021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525649021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525649021 none O=C(N[C@@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 13, 13, 13, 13, 13, 50, 50, 50, 50, 13, 4, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 6, 6, 6, 6, 6, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 77) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525649021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525649021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001525649021 none O=C(N[C@@H](c1cccc(OC(F)(F)F)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 11, 11, 11, 11, 11, 44, 44, 44, 44, 11, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525649021 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525649021 Building ZINC001525651221 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525651221 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/78 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3C(F)(F)F)CC2)cc1Cl) `ZINC001525651221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525651221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001525651221 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3C(F)(F)F)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 19, 19, 16, 19, 19, 19, 19, 19, 19, 16, 16, 6, 6, 6, 10, 10, 10, 6, 6, 16, 16, 16, 16, 16, 19, 19, 16, 19, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/79 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3C(F)(F)F)CC2)cc1Cl) `ZINC001525651221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525651221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001525651221 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3C(F)(F)F)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 20, 20, 18, 20, 20, 20, 20, 20, 20, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 20, 20, 18, 20, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525651221 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 Building ZINC001525651221 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525651221 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 78) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3C(F)(F)F)CC2)cc1Cl) `ZINC001525651221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525651221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001525651221 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3C(F)(F)F)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 19, 19, 16, 19, 19, 19, 19, 19, 19, 16, 16, 6, 6, 6, 10, 10, 10, 6, 6, 16, 16, 16, 16, 16, 19, 19, 16, 19, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 79) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3C(F)(F)F)CC2)cc1Cl) `ZINC001525651221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525651221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001525651221 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3C(F)(F)F)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 20, 20, 18, 20, 20, 20, 20, 20, 20, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 20, 20, 18, 20, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525651221 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525651221 Building ZINC001525660831 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525660831 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/80 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Br)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525660831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525660831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 28 natoms 27 natoms 26 natoms 25 names: ZINC001525660831 none O=C(Nc1cc(F)c(Br)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 17, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 31, 31, 31, 14, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 4, 31, 31, 11, 11] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/81 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Br)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525660831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525660831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 28 natoms 27 natoms 26 natoms 25 names: ZINC001525660831 none O=C(Nc1cc(F)c(Br)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 17, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 31, 31, 31, 14, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 4, 31, 31, 11, 11] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525660831 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 Building ZINC001525660831 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525660831 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 80) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Br)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525660831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525660831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 28 natoms 27 natoms 26 natoms 25 names: ZINC001525660831 none O=C(Nc1cc(F)c(Br)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 17, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 31, 31, 31, 14, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 4, 31, 31, 11, 11] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 81) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Br)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525660831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525660831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 28 natoms 27 natoms 26 natoms 25 names: ZINC001525660831 none O=C(Nc1cc(F)c(Br)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 17, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 31, 31, 31, 14, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 4, 31, 31, 11, 11] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525660831 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525660831 Building ZINC001525671952 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525671952 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/82 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C1) `ZINC001525671952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525671952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525671952 none CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 8, 5, 5, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 23, 15, 23, 15, 15, 15, 15, 8, 15, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 8, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 15, 3, 9, 9, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/83 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C1) `ZINC001525671952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525671952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525671952 none CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 8, 5, 5, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 23, 15, 23, 15, 15, 15, 15, 8, 15, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 8, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 15, 3, 9, 9, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525671952 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 Building ZINC001525671952 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525671952 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 82) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C1) `ZINC001525671952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525671952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525671952 none CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 8, 5, 5, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 23, 15, 23, 15, 15, 15, 15, 8, 15, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 8, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 15, 3, 9, 9, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 83) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C1) `ZINC001525671952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525671952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001525671952 none CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 8, 5, 5, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 23, 15, 23, 15, 15, 15, 15, 8, 15, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 8, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 15, 3, 9, 9, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525671952 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525671952 Building ZINC001525693625 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525693625 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/84 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)c2)c1) `ZINC001525693625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525693625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001525693625 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 50, 50, 45, 24, 24, 24, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 50, 50, 50, 50, 45, 50, 50, 50, 50, 24, 24, 24, 9, 9, 2, 2, 2, 2, 2, 24, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/85 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)c2)c1) `ZINC001525693625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525693625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001525693625 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 50, 50, 50, 50, 46, 24, 24, 24, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 50, 50, 50, 50, 46, 50, 50, 50, 50, 24, 24, 24, 9, 9, 2, 2, 2, 2, 2, 24, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525693625 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 Building ZINC001525693625 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525693625 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 84) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)c2)c1) `ZINC001525693625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525693625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001525693625 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 50, 50, 45, 24, 24, 24, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 50, 50, 50, 50, 45, 50, 50, 50, 50, 24, 24, 24, 9, 9, 2, 2, 2, 2, 2, 24, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 85) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)c2)c1) `ZINC001525693625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525693625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001525693625 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 50, 50, 50, 50, 46, 24, 24, 24, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 50, 50, 50, 50, 46, 50, 50, 50, 50, 24, 24, 24, 9, 9, 2, 2, 2, 2, 2, 24, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525693625 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525693625 Building ZINC001525700366 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525700366 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/86 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(Cl)cc(Br)c32)cc1Cl) `ZINC001525700366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525700366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001525700366 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(Cl)cc(Br)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 1, 12, 12, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 20, 20, 20, 12, 12, 10, 10, 10, 10, 10, 10, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/87 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(Cl)cc(Br)c32)cc1Cl) `ZINC001525700366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525700366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001525700366 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(Cl)cc(Br)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 1, 12, 12, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 16, 16, 16, 12, 12, 9, 9, 9, 9, 9, 9, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525700366 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 Building ZINC001525700366 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525700366 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 86) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(Cl)cc(Br)c32)cc1Cl) `ZINC001525700366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525700366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001525700366 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(Cl)cc(Br)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 1, 12, 12, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 20, 20, 20, 12, 12, 10, 10, 10, 10, 10, 10, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 87) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(Cl)cc(Br)c32)cc1Cl) `ZINC001525700366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525700366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001525700366 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(Cl)cc(Br)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 1, 12, 12, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 16, 16, 16, 12, 12, 9, 9, 9, 9, 9, 9, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525700366 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525700366 Building ZINC001525726103 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525726103 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/88 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2C(F)(F)F)CC2CC2)cc1Cl) `ZINC001525726103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525726103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001525726103 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2C(F)(F)F)CC2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 9, 9, 8, 9, 9, 9, 9, 9, 9, 5, 10, 14, 14, 6, 6, 6, 11, 11, 11, 6, 6, 8, 8, 9, 9, 8, 9, 10, 10, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/89 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2C(F)(F)F)CC2CC2)cc1Cl) `ZINC001525726103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525726103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001525726103 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2C(F)(F)F)CC2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 7, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 8, 8, 8, 8, 8, 8, 7, 7, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525726103 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 Building ZINC001525726103 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525726103 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 88) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2C(F)(F)F)CC2CC2)cc1Cl) `ZINC001525726103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525726103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001525726103 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2C(F)(F)F)CC2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 9, 9, 8, 9, 9, 9, 9, 9, 9, 5, 10, 14, 14, 6, 6, 6, 11, 11, 11, 6, 6, 8, 8, 9, 9, 8, 9, 10, 10, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 89) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2C(F)(F)F)CC2CC2)cc1Cl) `ZINC001525726103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525726103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001525726103 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2C(F)(F)F)CC2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 7, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 8, 8, 8, 8, 8, 8, 7, 7, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525726103 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726103 Building ZINC001525726137 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525726137 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/90 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(F)cc1Cl)CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525726137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525726137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001525726137 none O=C(N(Cc1ccc(F)cc1Cl)CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 12, 19, 19, 12, 19, 19, 19, 19, 6, 9, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 19, 19, 19, 9, 9, 17, 17, 17, 17, 17, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/91 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(F)cc1Cl)CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525726137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525726137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001525726137 none O=C(N(Cc1ccc(F)cc1Cl)CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 9, 16, 16, 9, 13, 16, 16, 16, 4, 8, 18, 18, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 16, 16, 16, 8, 8, 18, 18, 18, 18, 18, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525726137 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 Building ZINC001525726137 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525726137 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 90) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(F)cc1Cl)CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525726137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525726137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001525726137 none O=C(N(Cc1ccc(F)cc1Cl)CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 12, 19, 19, 12, 19, 19, 19, 19, 6, 9, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 19, 19, 19, 9, 9, 17, 17, 17, 17, 17, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 91) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(F)cc1Cl)CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525726137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525726137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001525726137 none O=C(N(Cc1ccc(F)cc1Cl)CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 9, 16, 16, 9, 13, 16, 16, 16, 4, 8, 18, 18, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 16, 16, 16, 8, 8, 18, 18, 18, 18, 18, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525726137 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525726137 Building ZINC001525763967 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525763967 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/92 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525763967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525763967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525763967 none O=C(NCc1ccccc1OCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 18, 18, 18, 18, 18, 18, 25, 44, 49, 49, 47, 49, 49, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 18, 18, 18, 18, 44, 44, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/93 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525763967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525763967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525763967 none O=C(NCc1ccccc1OCc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 17, 17, 17, 17, 17, 17, 24, 44, 49, 49, 46, 49, 49, 1, 1, 1, 4, 4, 4, 4, 4, 2, 9, 9, 17, 17, 17, 17, 44, 44, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525763967 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 Building ZINC001525763967 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525763967 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 92) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525763967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525763967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525763967 none O=C(NCc1ccccc1OCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 18, 18, 18, 18, 18, 18, 25, 44, 49, 49, 47, 49, 49, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 18, 18, 18, 18, 44, 44, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 93) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525763967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525763967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525763967 none O=C(NCc1ccccc1OCc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 17, 17, 17, 17, 17, 17, 24, 44, 49, 49, 46, 49, 49, 1, 1, 1, 4, 4, 4, 4, 4, 2, 9, 9, 17, 17, 17, 17, 44, 44, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525763967 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525763967 Building ZINC001525786547 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525786547 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/94 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001525786547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525786547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525786547 none CCOc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 14, 14, 14, 14, 14, 4, 4, 4, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/95 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001525786547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525786547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525786547 none CCOc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 14, 14, 14, 14, 14, 4, 4, 4, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525786547 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 Building ZINC001525786547 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525786547 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 94) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001525786547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525786547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525786547 none CCOc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 14, 14, 14, 14, 14, 4, 4, 4, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 95) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001525786547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525786547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525786547 none CCOc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 14, 14, 14, 14, 14, 4, 4, 4, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525786547 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525786547 Building ZINC001525787602 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525787602 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/96 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 33, 33, 39, 39, 39, 39, 39, 39, 33, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 46, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/97 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 36, 36, 34, 34, 36, 36, 34, 44, 44, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 36, 36, 36, 36, 44, 44, 44, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/98 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/98' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 33, 33, 39, 39, 39, 39, 39, 39, 33, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 46, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/99 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/99' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 36, 36, 34, 34, 36, 36, 34, 44, 44, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 36, 36, 36, 36, 44, 44, 44, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525787602 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 Building ZINC001525787602 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525787602 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 96) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 33, 33, 39, 39, 39, 39, 39, 39, 33, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 46, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 97) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 36, 36, 34, 34, 36, 36, 34, 44, 44, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 36, 36, 36, 36, 44, 44, 44, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 98) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 33, 33, 39, 39, 39, 39, 39, 39, 33, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 46, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 99) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 36, 36, 34, 34, 36, 36, 34, 44, 44, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 36, 36, 36, 36, 44, 44, 44, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525787602 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 Building ZINC001525787602 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525787602 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 96) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 33, 33, 39, 39, 39, 39, 39, 39, 33, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 46, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 97) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 36, 36, 34, 34, 36, 36, 34, 44, 44, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 36, 36, 36, 36, 44, 44, 44, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 98) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 33, 33, 39, 39, 39, 39, 39, 39, 33, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 46, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 99) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 36, 36, 34, 34, 36, 36, 34, 44, 44, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 36, 36, 36, 36, 44, 44, 44, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525787602 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 Building ZINC001525787602 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525787602 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 96) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 33, 33, 39, 39, 39, 39, 39, 39, 33, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 46, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 97) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 36, 36, 34, 34, 36, 36, 34, 44, 44, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 36, 36, 36, 36, 44, 44, 44, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 98) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 33, 33, 39, 39, 39, 39, 39, 39, 33, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 22, 22, 39, 39, 39, 39, 46, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 99) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787602.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525787602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787602 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 36, 36, 34, 34, 36, 36, 34, 44, 44, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 36, 36, 36, 36, 44, 44, 44, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525787602 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787602 Building ZINC001525787603 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525787603 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/100 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 38, 38, 34, 34, 38, 38, 34, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 38, 38, 38, 38, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/101 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 42, 42, 45, 45, 42, 42, 45, 45, 42, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/102 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/102' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 38, 38, 34, 34, 38, 38, 34, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 38, 38, 38, 38, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/103 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/103' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 42, 42, 45, 45, 42, 42, 45, 45, 42, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525787603 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 Building ZINC001525787603 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525787603 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 100) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 38, 38, 34, 34, 38, 38, 34, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 38, 38, 38, 38, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 101) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 42, 42, 45, 45, 42, 42, 45, 45, 42, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 102) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 38, 38, 34, 34, 38, 38, 34, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 38, 38, 38, 38, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 103) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 42, 42, 45, 45, 42, 42, 45, 45, 42, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525787603 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 Building ZINC001525787603 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525787603 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 100) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 38, 38, 34, 34, 38, 38, 34, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 38, 38, 38, 38, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 101) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 42, 42, 45, 45, 42, 42, 45, 45, 42, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 102) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 38, 38, 34, 34, 38, 38, 34, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 38, 38, 38, 38, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 103) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 42, 42, 45, 45, 42, 42, 45, 45, 42, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525787603 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 Building ZINC001525787603 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525787603 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 100) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 38, 38, 34, 34, 38, 38, 34, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 38, 38, 38, 38, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 101) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 42, 42, 45, 45, 42, 42, 45, 45, 42, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 102) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 38, 38, 34, 34, 38, 38, 34, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 38, 38, 38, 38, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 103) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F) `ZINC001525787603.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525787603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001525787603 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(Cl)cc1)N(C)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 42, 42, 45, 45, 42, 42, 45, 45, 42, 45, 45, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525787603 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525787603 Building ZINC001525794284 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525794284 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/104 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(Cl)c1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525794284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525794284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525794284 none O=C(N[C@@H](c1cccc(Cl)c1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 20, 20, 17, 20, 20, 20, 5, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 3, 20, 20, 20, 20, 18, 18, 18, 18, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/105 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(Cl)c1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525794284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525794284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525794284 none O=C(N[C@@H](c1cccc(Cl)c1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 20, 20, 16, 20, 20, 20, 6, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 3, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525794284 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 Building ZINC001525794284 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525794284 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 104) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(Cl)c1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525794284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525794284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525794284 none O=C(N[C@@H](c1cccc(Cl)c1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 20, 20, 17, 20, 20, 20, 5, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 3, 20, 20, 20, 20, 18, 18, 18, 18, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 105) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(Cl)c1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525794284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525794284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525794284 none O=C(N[C@@H](c1cccc(Cl)c1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 20, 20, 16, 20, 20, 20, 6, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 3, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525794284 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794284 Building ZINC001525794286 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525794286 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/106 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(Cl)c1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525794286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525794286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525794286 none O=C(N[C@H](c1cccc(Cl)c1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 20, 20, 15, 20, 20, 20, 6, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 3, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/107 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(Cl)c1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525794286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525794286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525794286 none O=C(N[C@H](c1cccc(Cl)c1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 20, 20, 20, 20, 20, 20, 5, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 3, 20, 20, 20, 20, 17, 17, 17, 17, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525794286 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 Building ZINC001525794286 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525794286 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 106) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(Cl)c1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525794286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525794286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525794286 none O=C(N[C@H](c1cccc(Cl)c1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 20, 20, 15, 20, 20, 20, 6, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 3, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 107) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(Cl)c1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001525794286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525794286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001525794286 none O=C(N[C@H](c1cccc(Cl)c1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 20, 20, 20, 20, 20, 20, 5, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 3, 20, 20, 20, 20, 17, 17, 17, 17, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525794286 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525794286 Building ZINC001525827206 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525827206 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/108 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(=O)n(Cc2ccccc2Cl)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001525827206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525827206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525827206 none O=C(Nc1ccc(=O)n(Cc2ccccc2Cl)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 32, 50, 50, 45, 50, 50, 50, 11, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 32, 32, 50, 50, 50, 50, 11, 2, 1, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/109 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(=O)n(Cc2ccccc2Cl)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001525827206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525827206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525827206 none O=C(Nc1ccc(=O)n(Cc2ccccc2Cl)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 32, 50, 50, 45, 50, 50, 50, 11, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 32, 32, 50, 50, 50, 50, 11, 2, 1, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525827206 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 Building ZINC001525827206 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525827206 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 108) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(=O)n(Cc2ccccc2Cl)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001525827206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525827206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525827206 none O=C(Nc1ccc(=O)n(Cc2ccccc2Cl)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 32, 50, 50, 45, 50, 50, 50, 11, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 32, 32, 50, 50, 50, 50, 11, 2, 1, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 109) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(=O)n(Cc2ccccc2Cl)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001525827206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525827206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001525827206 none O=C(Nc1ccc(=O)n(Cc2ccccc2Cl)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 32, 50, 50, 45, 50, 50, 50, 11, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 32, 32, 50, 50, 50, 50, 11, 2, 1, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525827206 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525827206 Building ZINC001525837122 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525837122 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/110 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cn2)c1) `ZINC001525837122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525837122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525837122 none COc1cccc(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 7, 7, 1, 1, 1, 1, 20, 50] 50 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/111 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cn2)c1) `ZINC001525837122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525837122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525837122 none COc1cccc(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 7, 7, 1, 1, 1, 1, 20, 50] 50 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525837122 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 Building ZINC001525837122 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525837122 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 110) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cn2)c1) `ZINC001525837122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525837122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525837122 none COc1cccc(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 7, 7, 1, 1, 1, 1, 20, 50] 50 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 111) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cn2)c1) `ZINC001525837122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525837122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525837122 none COc1cccc(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 7, 7, 1, 1, 1, 1, 20, 50] 50 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525837122 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525837122 Building ZINC001525869265 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525869265 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/112 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/112' -> `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(CCc1cccc(F)c1)C1CCCC1) `ZINC001525869265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525869265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001525869265 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1cccc(F)c1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 3, 7, 7, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 81 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/113 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/113' -> `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(CCc1cccc(F)c1)C1CCCC1) `ZINC001525869265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525869265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001525869265 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1cccc(F)c1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 8, 8, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525869265 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 Building ZINC001525869265 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525869265 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 112) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCc1cccc(F)c1)C1CCCC1) `ZINC001525869265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525869265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001525869265 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1cccc(F)c1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 3, 7, 7, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 81 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 113) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCc1cccc(F)c1)C1CCCC1) `ZINC001525869265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525869265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001525869265 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1cccc(F)c1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 8, 8, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525869265 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525869265 Building ZINC001525886300 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525886300 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/114 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001525886300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525886300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525886300 none O=C(N[C@@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 16, 16, 16, 16, 16, 16, 4, 15, 15, 10, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/115 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001525886300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525886300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525886300 none O=C(N[C@@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 15, 15, 15, 15, 15, 15, 4, 15, 15, 9, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525886300 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 Building ZINC001525886300 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525886300 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 114) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001525886300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525886300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525886300 none O=C(N[C@@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 16, 16, 16, 16, 16, 16, 4, 15, 15, 10, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 115) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001525886300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525886300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525886300 none O=C(N[C@@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 15, 15, 15, 15, 15, 15, 4, 15, 15, 9, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525886300 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886300 Building ZINC001525886301 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525886301 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/116 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001525886301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525886301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525886301 none O=C(N[C@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 15, 15, 15, 15, 15, 15, 4, 15, 15, 11, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/117 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001525886301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525886301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525886301 none O=C(N[C@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 16, 16, 16, 16, 16, 16, 4, 15, 15, 11, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525886301 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 Building ZINC001525886301 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525886301 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 116) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001525886301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525886301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525886301 none O=C(N[C@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 15, 15, 15, 15, 15, 15, 4, 15, 15, 11, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 117) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001525886301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525886301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001525886301 none O=C(N[C@H](c1cccc(F)c1)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 16, 16, 16, 16, 16, 16, 4, 15, 15, 11, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525886301 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525886301 Building ZINC001525889751 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525889751 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/118 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1)c1ccc(F)cc1) `ZINC001525889751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525889751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525889751 none O=C(Nc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 36, 36, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 36, 36, 48, 50, 50, 48, 48, 50, 50, 48, 36, 36, 13, 13, 2, 2, 1, 2, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/119 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1)c1ccc(F)cc1) `ZINC001525889751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525889751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525889751 none O=C(Nc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 34, 34, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 47, 50, 50, 47, 47, 50, 50, 47, 34, 34, 11, 11, 2, 3, 1, 3, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525889751 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 Building ZINC001525889751 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525889751 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 118) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1)c1ccc(F)cc1) `ZINC001525889751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525889751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525889751 none O=C(Nc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 36, 36, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 36, 36, 48, 50, 50, 48, 48, 50, 50, 48, 36, 36, 13, 13, 2, 2, 1, 2, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 119) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1)c1ccc(F)cc1) `ZINC001525889751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525889751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525889751 none O=C(Nc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 34, 34, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 47, 50, 50, 47, 47, 50, 50, 47, 34, 34, 11, 11, 2, 3, 1, 3, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525889751 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525889751 Building ZINC001525909687 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525909687 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/120 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC(F)F) `ZINC001525909687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525909687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525909687 none CCOc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 34, 12, 12, 12, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 35, 48, 48, 42, 42, 42, 42, 42, 12, 6, 6, 3, 3, 3, 1, 1, 1, 12, 12, 48] 50 rigid atoms, others: [39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/121 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC(F)F) `ZINC001525909687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525909687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525909687 none CCOc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 34, 12, 12, 12, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 35, 48, 48, 42, 42, 42, 42, 42, 12, 6, 6, 3, 3, 3, 1, 1, 1, 12, 12, 48] 50 rigid atoms, others: [39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525909687 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 Building ZINC001525909687 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525909687 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 120) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC(F)F) `ZINC001525909687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525909687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525909687 none CCOc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 34, 12, 12, 12, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 35, 48, 48, 42, 42, 42, 42, 42, 12, 6, 6, 3, 3, 3, 1, 1, 1, 12, 12, 48] 50 rigid atoms, others: [39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 121) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC(F)F) `ZINC001525909687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525909687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001525909687 none CCOc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 34, 12, 12, 12, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 35, 48, 48, 42, 42, 42, 42, 42, 12, 6, 6, 3, 3, 3, 1, 1, 1, 12, 12, 48] 50 rigid atoms, others: [39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525909687 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525909687 Building ZINC001525926359 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525926359 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/122 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001525926359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525926359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525926359 none CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 15, 35, 15, 15, 15, 15, 15, 23, 23, 16, 23, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 23, 23, 18, 23, 23, 3, 3, 1, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/123 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001525926359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525926359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525926359 none CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 15, 35, 15, 15, 15, 15, 15, 23, 23, 18, 23, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 23, 23, 20, 23, 23, 3, 3, 1, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525926359 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 Building ZINC001525926359 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525926359 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 122) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001525926359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525926359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525926359 none CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 15, 35, 15, 15, 15, 15, 15, 23, 23, 16, 23, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 23, 23, 18, 23, 23, 3, 3, 1, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 123) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001525926359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525926359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001525926359 none CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 15, 35, 15, 15, 15, 15, 15, 23, 23, 18, 23, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 23, 23, 20, 23, 23, 3, 3, 1, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525926359 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525926359 Building ZINC001525974494 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525974494 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/124 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2C)cc1Cl) `ZINC001525974494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525974494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001525974494 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 10, 10, 14, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/125 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2C)cc1Cl) `ZINC001525974494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525974494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001525974494 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 9, 9, 13, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525974494 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 Building ZINC001525974494 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525974494 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 124) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2C)cc1Cl) `ZINC001525974494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525974494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001525974494 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 10, 10, 14, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 125) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2C)cc1Cl) `ZINC001525974494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525974494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001525974494 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 9, 9, 13, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001525974494 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001525974494 Building ZINC001526011910 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526011910 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/126 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1cccc(F)c1) `ZINC001526011910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526011910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526011910 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 18, 42, 42, 42, 42, 42, 42, 4, 4, 4, 2, 5, 5, 18, 18, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/127 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1cccc(F)c1) `ZINC001526011910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526011910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526011910 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 18, 42, 42, 42, 42, 42, 42, 4, 4, 4, 2, 5, 5, 18, 18, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526011910 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 Building ZINC001526011910 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526011910 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 126) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1cccc(F)c1) `ZINC001526011910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526011910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526011910 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 18, 42, 42, 42, 42, 42, 42, 4, 4, 4, 2, 5, 5, 18, 18, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 127) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1cccc(F)c1) `ZINC001526011910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526011910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526011910 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 18, 42, 42, 42, 42, 42, 42, 4, 4, 4, 2, 5, 5, 18, 18, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526011910 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526011910 Building ZINC001526013312 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526013312 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/128 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(F)cc1) `ZINC001526013312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526013312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526013312 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 21, 29, 29, 29, 29, 29, 29, 5, 5, 5, 3, 7, 7, 21, 21, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/129 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(F)cc1) `ZINC001526013312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526013312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526013312 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 21, 29, 29, 21, 29, 29, 29, 5, 5, 5, 3, 7, 7, 21, 21, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526013312 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 Building ZINC001526013312 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526013312 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 128) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(F)cc1) `ZINC001526013312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526013312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526013312 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 21, 29, 29, 29, 29, 29, 29, 5, 5, 5, 3, 7, 7, 21, 21, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 129) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(F)cc1) `ZINC001526013312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526013312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526013312 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 21, 29, 29, 21, 29, 29, 29, 5, 5, 5, 3, 7, 7, 21, 21, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526013312 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526013312 Building ZINC001526016010 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526016010 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/130 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)sc1Cc1cccc(Br)c1) `ZINC001526016010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526016010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526016010 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)sc1Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 19, 50, 50, 50, 50, 50, 50, 4, 4, 4, 2, 2, 2, 2, 2, 19, 19, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/131 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)sc1Cc1cccc(Br)c1) `ZINC001526016010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526016010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526016010 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)sc1Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 19, 50, 50, 50, 50, 50, 50, 4, 4, 4, 2, 2, 2, 2, 2, 19, 19, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526016010 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 Building ZINC001526016010 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526016010 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 130) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)sc1Cc1cccc(Br)c1) `ZINC001526016010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526016010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526016010 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)sc1Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 19, 50, 50, 50, 50, 50, 50, 4, 4, 4, 2, 2, 2, 2, 2, 19, 19, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 131) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)sc1Cc1cccc(Br)c1) `ZINC001526016010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526016010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526016010 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)sc1Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 19, 50, 50, 50, 50, 50, 50, 4, 4, 4, 2, 2, 2, 2, 2, 19, 19, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526016010 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526016010 Building ZINC001526081254 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526081254 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/132 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCCC3)cn1) `ZINC001526081254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526081254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001526081254 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 17, 11, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 72 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/133 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCCC3)cn1) `ZINC001526081254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526081254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001526081254 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 11, 11, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 96 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526081254 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 Building ZINC001526081254 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526081254 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 132) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCCC3)cn1) `ZINC001526081254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526081254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001526081254 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 17, 11, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 72 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 133) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCCC3)cn1) `ZINC001526081254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526081254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001526081254 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 11, 11, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 96 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526081254 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526081254 Building ZINC001526093348 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526093348 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/134 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCC2) `ZINC001526093348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526093348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526093348 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 40, 40, 40, 40, 40, 40, 40, 40, 26, 26, 26, 26, 5, 5, 5, 4, 4, 4, 4, 7, 40, 40, 40, 40, 40, 40, 40, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/135 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCC2) `ZINC001526093348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526093348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526093348 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 5, 5, 5, 4, 4, 4, 4, 7, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526093348 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 Building ZINC001526093348 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526093348 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 134) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCC2) `ZINC001526093348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526093348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526093348 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 40, 40, 40, 40, 40, 40, 40, 40, 26, 26, 26, 26, 5, 5, 5, 4, 4, 4, 4, 7, 40, 40, 40, 40, 40, 40, 40, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 135) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCC2) `ZINC001526093348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526093348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526093348 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 5, 5, 5, 4, 4, 4, 4, 7, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526093348 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526093348 Building ZINC001526130916 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526130916 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/136 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/136' -> `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)Nc1cccc2c(Br)ccnc12) `ZINC001526130916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526130916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526130916 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 13, 13, 6, 13, 13, 4, 4, 4, 6, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/137 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/137' -> `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)Nc1cccc2c(Br)ccnc12) `ZINC001526130916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526130916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526130916 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 6, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526130916 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 Building ZINC001526130916 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526130916 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 136) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1cccc2c(Br)ccnc12) `ZINC001526130916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526130916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526130916 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 13, 13, 6, 13, 13, 4, 4, 4, 6, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 137) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1cccc2c(Br)ccnc12) `ZINC001526130916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526130916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526130916 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 6, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526130916 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526130916 Building ZINC001526142591 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526142591 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/138 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Br)ccnc12)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526142591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526142591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526142591 none O=C(Nc1cccc2c(Br)ccnc12)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 6, 27, 27, 27, 27, 27, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/139 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Br)ccnc12)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526142591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526142591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526142591 none O=C(Nc1cccc2c(Br)ccnc12)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 6, 27, 27, 27, 27, 27, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526142591 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 Building ZINC001526142591 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526142591 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 138) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Br)ccnc12)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526142591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526142591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526142591 none O=C(Nc1cccc2c(Br)ccnc12)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 6, 27, 27, 27, 27, 27, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 139) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Br)ccnc12)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526142591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526142591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526142591 none O=C(Nc1cccc2c(Br)ccnc12)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 6, 27, 27, 27, 27, 27, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526142591 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526142591 Building ZINC001526203825 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526203825 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/140 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccn1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526203825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526203825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526203825 none O=C(N(Cc1ccccn1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 19, 31, 31, 31, 31, 31, 7, 13, 13, 7, 11, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 31, 31, 31, 31, 13, 13, 13, 13, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/141 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccn1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526203825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526203825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526203825 none O=C(N(Cc1ccccn1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 20, 32, 32, 32, 32, 32, 7, 14, 14, 10, 11, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 32, 32, 32, 32, 14, 14, 14, 14, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526203825 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 Building ZINC001526203825 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526203825 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 140) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccn1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526203825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526203825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526203825 none O=C(N(Cc1ccccn1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 19, 31, 31, 31, 31, 31, 7, 13, 13, 7, 11, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 31, 31, 31, 31, 13, 13, 13, 13, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 141) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccn1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526203825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526203825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001526203825 none O=C(N(Cc1ccccn1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 20, 32, 32, 32, 32, 32, 7, 14, 14, 10, 11, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 32, 32, 32, 32, 14, 14, 14, 14, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526203825 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526203825 Building ZINC001526225030 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526225030 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/142 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCc1ccc(C(F)(F)F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526225030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526225030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526225030 none CCN(CCc1ccc(C(F)(F)F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 5, 9, 14, 16, 23, 23, 16, 23, 23, 23, 23, 23, 23, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 16, 16, 23, 23, 23, 23, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/143 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCc1ccc(C(F)(F)F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526225030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526225030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526225030 none CCN(CCc1ccc(C(F)(F)F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 5, 10, 16, 18, 28, 28, 18, 25, 28, 28, 28, 28, 28, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 18, 18, 28, 28, 28, 28, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526225030 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 Building ZINC001526225030 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526225030 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 142) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCc1ccc(C(F)(F)F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526225030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526225030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526225030 none CCN(CCc1ccc(C(F)(F)F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 5, 9, 14, 16, 23, 23, 16, 23, 23, 23, 23, 23, 23, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 16, 16, 23, 23, 23, 23, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 143) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCc1ccc(C(F)(F)F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526225030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526225030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526225030 none CCN(CCc1ccc(C(F)(F)F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 5, 10, 16, 18, 28, 28, 18, 25, 28, 28, 28, 28, 28, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 18, 18, 28, 28, 28, 28, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526225030 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526225030 Building ZINC001526231438 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526231438 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/144 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc(OC)c(OC)c2)C2CCCCC2)cc1Cl) `ZINC001526231438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526231438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526231438 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc(OC)c(OC)c2)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 4, 8, 8, 8, 8, 17, 8, 8, 20, 8, 3, 3, 3, 3, 3, 3, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 8, 8, 17, 17, 17, 20, 20, 20, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/145 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc(OC)c(OC)c2)C2CCCCC2)cc1Cl) `ZINC001526231438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526231438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526231438 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc(OC)c(OC)c2)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 4, 8, 8, 8, 8, 15, 8, 8, 20, 8, 3, 3, 3, 3, 3, 3, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 8, 8, 15, 15, 15, 20, 20, 20, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526231438 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 Building ZINC001526231438 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526231438 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 144) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc(OC)c(OC)c2)C2CCCCC2)cc1Cl) `ZINC001526231438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526231438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526231438 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc(OC)c(OC)c2)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 4, 8, 8, 8, 8, 17, 8, 8, 20, 8, 3, 3, 3, 3, 3, 3, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 8, 8, 17, 17, 17, 20, 20, 20, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 145) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc(OC)c(OC)c2)C2CCCCC2)cc1Cl) `ZINC001526231438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526231438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526231438 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc(OC)c(OC)c2)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 4, 8, 8, 8, 8, 15, 8, 8, 20, 8, 3, 3, 3, 3, 3, 3, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 8, 8, 15, 15, 15, 20, 20, 20, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526231438 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526231438 Building ZINC001526266703 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526266703 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/146 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cccc(C)c1C) `ZINC001526266703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526266703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001526266703 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cccc(C)c1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 9, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 70 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/147 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cccc(C)c1C) `ZINC001526266703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526266703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001526266703 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cccc(C)c1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 9, 12, 12, 12, 12, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 5, 5, 5, 12, 12, 9, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526266703 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 Building ZINC001526266703 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526266703 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 146) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cccc(C)c1C) `ZINC001526266703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526266703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001526266703 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cccc(C)c1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 9, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 70 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 147) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cccc(C)c1C) `ZINC001526266703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526266703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001526266703 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cccc(C)c1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 9, 12, 12, 12, 12, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 5, 5, 5, 12, 12, 9, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526266703 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526266703 Building ZINC001526280430 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526280430 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/148 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 27, 34, 34, 29, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 34, 34, 34, 34, 34, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/149 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 27, 34, 34, 29, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 34, 34, 34, 34, 34, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/150 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/150' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 28, 34, 34, 31, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 28, 28, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/151 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/151' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 28, 34, 34, 31, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 28, 28, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526280430 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 Building ZINC001526280430 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526280430 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 148) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 27, 34, 34, 29, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 34, 34, 34, 34, 34, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 149) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 27, 34, 34, 29, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 34, 34, 34, 34, 34, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 150) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 28, 34, 34, 31, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 28, 28, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 151) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 28, 34, 34, 31, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 28, 28, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526280430 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 Building ZINC001526280430 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526280430 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 148) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 27, 34, 34, 29, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 34, 34, 34, 34, 34, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 149) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 27, 34, 34, 29, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 34, 34, 34, 34, 34, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 150) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 28, 34, 34, 31, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 28, 28, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 151) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 28, 34, 34, 31, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 28, 28, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526280430 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 Building ZINC001526280430 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526280430 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 148) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 27, 34, 34, 29, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 34, 34, 34, 34, 34, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 149) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 27, 34, 34, 29, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 34, 34, 34, 34, 34, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 150) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 28, 34, 34, 31, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 28, 28, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 151) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526280430.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526280430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526280430 none O=C(N1CCN(Cc2ccccc2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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: [5, 3, 8, 8, 8, 8, 8, 28, 34, 34, 31, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 28, 28, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526280430 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526280430 Building ZINC001526288566 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526288566 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/152 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(COc1ncc(Cl)cc1Cl)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526288566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526288566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526288566 none CC(C)(COc1ncc(Cl)cc1Cl)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 8, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 23, 41, 47, 47, 47, 47, 47, 47, 47, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 23, 23, 47, 47, 3, 3, 1, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/153 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(COc1ncc(Cl)cc1Cl)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526288566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526288566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526288566 none CC(C)(COc1ncc(Cl)cc1Cl)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 8, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 23, 41, 47, 47, 47, 47, 47, 47, 47, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 23, 23, 47, 47, 3, 3, 1, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526288566 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 Building ZINC001526288566 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526288566 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 152) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(COc1ncc(Cl)cc1Cl)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526288566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526288566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526288566 none CC(C)(COc1ncc(Cl)cc1Cl)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 8, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 23, 41, 47, 47, 47, 47, 47, 47, 47, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 23, 23, 47, 47, 3, 3, 1, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 153) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(COc1ncc(Cl)cc1Cl)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526288566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526288566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001526288566 none CC(C)(COc1ncc(Cl)cc1Cl)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 8, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 23, 41, 47, 47, 47, 47, 47, 47, 47, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 23, 23, 47, 47, 3, 3, 1, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526288566 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526288566 Building ZINC001526355380 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526355380 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/154 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/154' -> `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)Nc1ccc(N2CCCCC2)c(Cl)c1) `ZINC001526355380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526355380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001526355380 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 6, 6, 6, 22, 22, 16, 31, 39, 39, 39, 39, 39, 22, 22, 22, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 6, 22, 22, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/155 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/155' -> `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)Nc1ccc(N2CCCCC2)c(Cl)c1) `ZINC001526355380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526355380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001526355380 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 29, 38, 38, 38, 38, 38, 19, 19, 19, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 19, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526355380 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 Building ZINC001526355380 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526355380 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 154) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccc(N2CCCCC2)c(Cl)c1) `ZINC001526355380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526355380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001526355380 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 6, 6, 6, 22, 22, 16, 31, 39, 39, 39, 39, 39, 22, 22, 22, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 6, 22, 22, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 155) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccc(N2CCCCC2)c(Cl)c1) `ZINC001526355380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526355380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001526355380 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 29, 38, 38, 38, 38, 38, 19, 19, 19, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 19, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526355380 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526355380 Building ZINC001526392507 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526392507 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/156 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1) `ZINC001526392507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526392507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001526392507 none CC(C)(C)c1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 8, 11, 11, 8, 4, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 4, 10, 10, 10, 10, 10, 10, 10, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/157 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1) `ZINC001526392507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526392507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001526392507 none CC(C)(C)c1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 21, 20, 10, 12, 12, 8, 4, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 11, 11, 10, 11, 11, 10, 8, 8, 8, 8, 12, 12, 21, 20, 21, 21, 21, 21, 20, 20, 21, 12, 12, 4, 10, 11, 11, 10, 11, 11, 10, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526392507 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 Building ZINC001526392507 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526392507 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 156) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1) `ZINC001526392507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526392507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001526392507 none CC(C)(C)c1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 8, 11, 11, 8, 4, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 4, 10, 10, 10, 10, 10, 10, 10, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 157) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1) `ZINC001526392507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526392507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001526392507 none CC(C)(C)c1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 21, 20, 10, 12, 12, 8, 4, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 11, 11, 10, 11, 11, 10, 8, 8, 8, 8, 12, 12, 21, 20, 21, 21, 21, 21, 20, 20, 21, 12, 12, 4, 10, 11, 11, 10, 11, 11, 10, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526392507 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392507 Building ZINC001526392510 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526392510 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/158 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1) `ZINC001526392510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526392510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001526392510 none CC(C)(C)c1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 11, 13, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 11, 11, 10, 11, 11, 10, 8, 8, 8, 8, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 4, 10, 11, 11, 10, 11, 11, 10, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/159 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1) `ZINC001526392510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526392510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001526392510 none CC(C)(C)c1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 19, 11, 13, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 4, 10, 10, 10, 10, 10, 10, 10, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526392510 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 Building ZINC001526392510 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526392510 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 158) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1) `ZINC001526392510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526392510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001526392510 none CC(C)(C)c1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 11, 13, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 11, 11, 10, 11, 11, 10, 8, 8, 8, 8, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 4, 10, 11, 11, 10, 11, 11, 10, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 159) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1) `ZINC001526392510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526392510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001526392510 none CC(C)(C)c1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 19, 11, 13, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 4, 10, 10, 10, 10, 10, 10, 10, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526392510 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526392510 Building ZINC001526463413 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526463413 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/160 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526463413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526463413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001526463413 none O=C(Nc1cc(Cl)ccc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 5, 7, 7, 7, 26, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 3, 7, 6, 7, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/161 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526463413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526463413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001526463413 none O=C(Nc1cc(Cl)ccc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 3, 7, 7, 7, 26, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 3, 7, 5, 7, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526463413 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 Building ZINC001526463413 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526463413 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 160) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526463413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526463413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001526463413 none O=C(Nc1cc(Cl)ccc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 5, 7, 7, 7, 26, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 3, 7, 6, 7, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 161) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526463413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526463413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001526463413 none O=C(Nc1cc(Cl)ccc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 3, 7, 7, 7, 26, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 3, 7, 5, 7, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526463413 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526463413 Building ZINC001526505489 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526505489 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/162 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1cccc(Br)c1) `ZINC001526505489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526505489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001526505489 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 16, 16, 10, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 6, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/163 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1cccc(Br)c1) `ZINC001526505489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526505489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001526505489 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 11, 18, 18, 10, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 10, 10, 5, 5, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526505489 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 Building ZINC001526505489 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526505489 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 162) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1cccc(Br)c1) `ZINC001526505489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526505489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001526505489 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 16, 16, 10, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 6, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 163) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1cccc(Br)c1) `ZINC001526505489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526505489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001526505489 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 11, 18, 18, 10, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 10, 10, 5, 5, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526505489 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526505489 Building ZINC001526534268 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526534268 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/164 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/165 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/166 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/166' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/167 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/167' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526534268 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 Building ZINC001526534268 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526534268 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 164) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 165) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 166) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 167) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526534268 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 Building ZINC001526534268 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526534268 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 164) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 165) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 166) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 167) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526534268 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 Building ZINC001526534268 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526534268 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 164) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 165) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 166) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 167) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526534268.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526534268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526534268 none O=C(Nc1ccnc(N2CCc3ccccc3C2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526534268 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526534268 Building ZINC001526618552 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526618552 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/168 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1c1ccccc1) `ZINC001526618552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526618552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001526618552 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1c1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 7, 7, 7, 7, 2, 2, 2, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/169 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1c1ccccc1) `ZINC001526618552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526618552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001526618552 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1c1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526618552 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 Building ZINC001526618552 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526618552 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 168) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1c1ccccc1) `ZINC001526618552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526618552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001526618552 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1c1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 7, 7, 7, 7, 2, 2, 2, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 169) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1c1ccccc1) `ZINC001526618552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526618552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001526618552 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1c1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526618552 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526618552 Building ZINC001526632084 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526632084 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/170 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OCC) `ZINC001526632084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526632084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001526632084 none CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 20, 23, 26, 26, 26, 26, 26, 6, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/171 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OCC) `ZINC001526632084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526632084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001526632084 none CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 19, 21, 27, 27, 27, 27, 27, 6, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526632084 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 Building ZINC001526632084 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526632084 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 170) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OCC) `ZINC001526632084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526632084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001526632084 none CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 20, 23, 26, 26, 26, 26, 26, 6, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 171) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OCC) `ZINC001526632084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526632084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001526632084 none CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 19, 21, 27, 27, 27, 27, 27, 6, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526632084 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526632084 Building ZINC001526640945 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526640945 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/172 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(COc3cccc(F)c3)cc2)cc1Cl) `ZINC001526640945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526640945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001526640945 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(COc3cccc(F)c3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 6, 8, 19, 19, 30, 30, 30, 30, 30, 30, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 19, 19, 30, 30, 30, 30, 8, 8, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/173 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(COc3cccc(F)c3)cc2)cc1Cl) `ZINC001526640945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526640945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001526640945 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(COc3cccc(F)c3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 8, 19, 19, 31, 31, 31, 31, 31, 31, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 19, 19, 31, 31, 31, 31, 8, 8, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526640945 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 Building ZINC001526640945 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526640945 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 172) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(COc3cccc(F)c3)cc2)cc1Cl) `ZINC001526640945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526640945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001526640945 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(COc3cccc(F)c3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 6, 8, 19, 19, 30, 30, 30, 30, 30, 30, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 19, 19, 30, 30, 30, 30, 8, 8, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 173) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(COc3cccc(F)c3)cc2)cc1Cl) `ZINC001526640945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526640945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001526640945 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(COc3cccc(F)c3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 8, 19, 19, 31, 31, 31, 31, 31, 31, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 19, 19, 31, 31, 31, 31, 8, 8, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/150923/xbj-8058088.36/working/building/ZINC001526640945 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526640945 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526640945 Building ZINC001526685226 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526685226 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/174 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccccc2Cl)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526685226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526685226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526685226 none O=C(Nc1nnc(c2ccccc2Cl)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 30, 30, 10, 30, 30, 30, 7, 1, 1, 1, 10, 10, 10, 10, 10, 4, 30, 30, 16, 30, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/175 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccccc2Cl)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526685226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526685226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526685226 none O=C(Nc1nnc(c2ccccc2Cl)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 31, 31, 9, 31, 31, 31, 7, 1, 1, 1, 10, 10, 10, 10, 10, 4, 31, 31, 17, 31, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526685226 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 Building ZINC001526685226 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526685226 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 174) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccccc2Cl)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526685226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526685226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526685226 none O=C(Nc1nnc(c2ccccc2Cl)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 30, 30, 10, 30, 30, 30, 7, 1, 1, 1, 10, 10, 10, 10, 10, 4, 30, 30, 16, 30, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 175) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccccc2Cl)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526685226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526685226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526685226 none O=C(Nc1nnc(c2ccccc2Cl)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 31, 31, 9, 31, 31, 31, 7, 1, 1, 1, 10, 10, 10, 10, 10, 4, 31, 31, 17, 31, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526685226 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526685226 Building ZINC001526686615 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526686615 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/176 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccn(c2cccc(C(F)(F)F)c2)n1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526686615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526686615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001526686615 none O=C(Nc1ccn(c2cccc(C(F)(F)F)c2)n1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 1, 1, 1, 10, 10, 10, 10, 10, 5, 11, 11, 30, 30, 30, 30, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/177 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccn(c2cccc(C(F)(F)F)c2)n1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526686615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526686615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001526686615 none O=C(Nc1ccn(c2cccc(C(F)(F)F)c2)n1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 1, 1, 1, 10, 10, 10, 10, 10, 5, 10, 10, 32, 32, 32, 32, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526686615 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 Building ZINC001526686615 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526686615 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 176) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccn(c2cccc(C(F)(F)F)c2)n1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526686615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526686615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001526686615 none O=C(Nc1ccn(c2cccc(C(F)(F)F)c2)n1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 1, 1, 1, 10, 10, 10, 10, 10, 5, 11, 11, 30, 30, 30, 30, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 177) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccn(c2cccc(C(F)(F)F)c2)n1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526686615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526686615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001526686615 none O=C(Nc1ccn(c2cccc(C(F)(F)F)c2)n1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 1, 1, 1, 10, 10, 10, 10, 10, 5, 10, 10, 32, 32, 32, 32, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526686615 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526686615 Building ZINC001526697058 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526697058 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/178 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc3c(c2)OCO3)CCCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526697058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526697058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001526697058 none O=C(NCC1(c2ccc3c(c2)OCO3)CCCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 17, 32, 49, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 9, 9, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/179 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc3c(c2)OCO3)CCCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526697058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526697058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001526697058 none O=C(NCC1(c2ccc3c(c2)OCO3)CCCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 16, 35, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 9, 9, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526697058 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 Building ZINC001526697058 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526697058 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 178) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc3c(c2)OCO3)CCCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526697058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526697058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001526697058 none O=C(NCC1(c2ccc3c(c2)OCO3)CCCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 17, 32, 49, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 9, 9, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 179) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc3c(c2)OCO3)CCCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526697058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526697058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001526697058 none O=C(NCC1(c2ccc3c(c2)OCO3)CCCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 16, 35, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 9, 9, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526697058 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526697058 Building ZINC001526718657 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526718657 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/180 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/180' -> `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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 15, 15, 23, 30, 30, 26, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/181 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/181' -> `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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 14, 14, 24, 35, 35, 27, 35, 35, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 6, 6, 6, 6, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/182 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/182' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 15, 15, 23, 30, 30, 26, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/183 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/183' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 14, 14, 24, 35, 35, 27, 35, 35, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 6, 6, 6, 6, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526718657 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 Building ZINC001526718657 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526718657 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 180) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 15, 15, 23, 30, 30, 26, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 181) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 14, 14, 24, 35, 35, 27, 35, 35, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 6, 6, 6, 6, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 182) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 15, 15, 23, 30, 30, 26, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 183) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 14, 14, 24, 35, 35, 27, 35, 35, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 6, 6, 6, 6, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526718657 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 Building ZINC001526718657 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526718657 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 180) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 15, 15, 23, 30, 30, 26, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 181) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 14, 14, 24, 35, 35, 27, 35, 35, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 6, 6, 6, 6, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 182) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 15, 15, 23, 30, 30, 26, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 183) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 14, 14, 24, 35, 35, 27, 35, 35, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 6, 6, 6, 6, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526718657 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 Building ZINC001526718657 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526718657 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 180) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 15, 15, 23, 30, 30, 26, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 181) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 14, 14, 24, 35, 35, 27, 35, 35, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 6, 6, 6, 6, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 182) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 15, 15, 23, 30, 30, 26, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 23, 23, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 183) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccccc1N(C)Cc1ccccc1) `ZINC001526718657.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526718657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001526718657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 14, 14, 24, 35, 35, 27, 35, 35, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 6, 6, 6, 6, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526718657 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526718657 Building ZINC001526722842 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526722842 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/184 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1S(=O)(=O)C1CCCC1) `ZINC001526722842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526722842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526722842 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1S(=O)(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 31, 31, 44, 44, 44, 44, 44, 14, 14, 14, 14, 14, 2, 3, 1, 3, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/185 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1S(=O)(=O)C1CCCC1) `ZINC001526722842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526722842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526722842 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1S(=O)(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 28, 28, 42, 43, 43, 43, 43, 14, 14, 14, 14, 14, 2, 3, 1, 3, 14, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 145 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526722842 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 Building ZINC001526722842 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526722842 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 184) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1S(=O)(=O)C1CCCC1) `ZINC001526722842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526722842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526722842 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1S(=O)(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 31, 31, 44, 44, 44, 44, 44, 14, 14, 14, 14, 14, 2, 3, 1, 3, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 185) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1S(=O)(=O)C1CCCC1) `ZINC001526722842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526722842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526722842 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1S(=O)(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 28, 28, 42, 43, 43, 43, 43, 14, 14, 14, 14, 14, 2, 3, 1, 3, 14, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 145 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526722842 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526722842 Building ZINC001526727299 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526727299 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/186 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C2CC2)n1) `ZINC001526727299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526727299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001526727299 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C2CC2)n1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 11, 11, 7, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 5, 7, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/187 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C2CC2)n1) `ZINC001526727299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526727299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001526727299 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C2CC2)n1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 13, 13, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 5, 8, 8, 8, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 89 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526727299 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 Building ZINC001526727299 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526727299 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 186) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C2CC2)n1) `ZINC001526727299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526727299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001526727299 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C2CC2)n1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 11, 11, 7, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 5, 7, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 187) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C2CC2)n1) `ZINC001526727299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526727299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001526727299 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C2CC2)n1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 13, 13, 8, 3, 3, 3, 24, 24, 3, 24, 3, 3, 3, 5, 8, 8, 8, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 89 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526727299 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526727299 Building ZINC001526743833 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526743833 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/188 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)c(OC(C)(C)C)c(F)c1) `ZINC001526743833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526743833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001526743833 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)c(OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 5, 10, 26, 38, 38, 38, 14, 14, 14, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 4, 5, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/189 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)c(OC(C)(C)C)c(F)c1) `ZINC001526743833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526743833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001526743833 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)c(OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 8, 8, 20, 31, 31, 31, 11, 11, 11, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 4, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526743833 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 Building ZINC001526743833 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526743833 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 188) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)c(OC(C)(C)C)c(F)c1) `ZINC001526743833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526743833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001526743833 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)c(OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 5, 10, 26, 38, 38, 38, 14, 14, 14, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 4, 5, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 189) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)c(OC(C)(C)C)c(F)c1) `ZINC001526743833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526743833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001526743833 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)c(OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 8, 8, 20, 31, 31, 31, 11, 11, 11, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 4, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526743833 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526743833 Building ZINC001526827095 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526827095 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/190 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc2[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526827095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526827095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001526827095 none O=C(N1CCc2ccccc2[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 14, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 14, 25, 25, 12, 12] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/191 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc2[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526827095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526827095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001526827095 none O=C(N1CCc2ccccc2[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 13, 19, 19, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 13, 19, 19, 10, 10] 38 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526827095 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 Building ZINC001526827095 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526827095 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 190) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc2[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526827095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526827095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001526827095 none O=C(N1CCc2ccccc2[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 14, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 14, 25, 25, 12, 12] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 191) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc2[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526827095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526827095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001526827095 none O=C(N1CCc2ccccc2[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 13, 19, 19, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 13, 19, 19, 10, 10] 38 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526827095 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526827095 Building ZINC001526868740 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526868740 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/192 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 129 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/193 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 129 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/194 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/194' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/195 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/195' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526868740 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 Building ZINC001526868740 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526868740 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 192) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 129 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 193) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 129 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 194) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 195) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526868740 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 Building ZINC001526868740 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526868740 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 192) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 129 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 193) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 129 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 194) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 195) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526868740 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 Building ZINC001526868740 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526868740 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 192) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 129 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 193) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 129 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 194) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 195) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868740.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526868740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868740 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 26, 26, 26, 26, 26, 26, 5, 5, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526868740 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868740 Building ZINC001526868741 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526868741 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/196 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 10, 16, 26, 26, 26, 26, 26, 26, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/197 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 10, 16, 26, 26, 26, 26, 26, 26, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/198 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/198' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 8, 14, 25, 26, 26, 25, 26, 26, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 8, 8, 14, 14, 25, 25, 26, 26, 25, 26, 26, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/199 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/199' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 8, 14, 25, 26, 26, 25, 26, 26, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 8, 8, 14, 14, 25, 25, 26, 26, 25, 26, 26, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526868741 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 Building ZINC001526868741 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526868741 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 196) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 10, 16, 26, 26, 26, 26, 26, 26, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 197) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 10, 16, 26, 26, 26, 26, 26, 26, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 198) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 8, 14, 25, 26, 26, 25, 26, 26, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 8, 8, 14, 14, 25, 25, 26, 26, 25, 26, 26, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 199) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 8, 14, 25, 26, 26, 25, 26, 26, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 8, 8, 14, 14, 25, 25, 26, 26, 25, 26, 26, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526868741 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 Building ZINC001526868741 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526868741 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 196) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 10, 16, 26, 26, 26, 26, 26, 26, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 197) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 10, 16, 26, 26, 26, 26, 26, 26, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 198) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 8, 14, 25, 26, 26, 25, 26, 26, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 8, 8, 14, 14, 25, 25, 26, 26, 25, 26, 26, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 199) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 8, 14, 25, 26, 26, 25, 26, 26, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 8, 8, 14, 14, 25, 25, 26, 26, 25, 26, 26, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526868741 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 Building ZINC001526868741 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526868741 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 196) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 10, 16, 26, 26, 26, 26, 26, 26, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 197) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 10, 16, 26, 26, 26, 26, 26, 26, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 198) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 8, 14, 25, 26, 26, 25, 26, 26, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 8, 8, 14, 14, 25, 25, 26, 26, 25, 26, 26, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 199) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001526868741.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526868741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001526868741 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 8, 14, 25, 26, 26, 25, 26, 26, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 8, 8, 14, 14, 25, 25, 26, 26, 25, 26, 26, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526868741 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526868741 Building ZINC001526887952 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526887952 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/200 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](C)C2) `ZINC001526887952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526887952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526887952 none CC(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', '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, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 30, 27, 10, 27, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/201 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](C)C2) `ZINC001526887952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526887952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526887952 none CC(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', '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, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 28, 9, 28, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526887952 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 Building ZINC001526887952 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526887952 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 200) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](C)C2) `ZINC001526887952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526887952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526887952 none CC(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', '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, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 30, 27, 10, 27, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 201) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](C)C2) `ZINC001526887952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526887952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526887952 none CC(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', '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, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 28, 9, 28, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526887952 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887952 Building ZINC001526887953 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526887953 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/202 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](C)C2) `ZINC001526887953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526887953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526887953 none CC(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', '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, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 33, 25, 6, 25, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 6, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/203 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](C)C2) `ZINC001526887953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526887953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526887953 none CC(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', '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, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 29, 21, 6, 21, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 6, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526887953 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 Building ZINC001526887953 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526887953 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 202) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](C)C2) `ZINC001526887953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526887953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526887953 none CC(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', '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, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 33, 25, 6, 25, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 6, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 203) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](C)C2) `ZINC001526887953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526887953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526887953 none CC(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', '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, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 29, 21, 6, 21, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 6, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526887953 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526887953 Building ZINC001526904269 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526904269 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/204 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1cccc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526904269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526904269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001526904269 none O=C(Nc1ccnn1Cc1cccc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 11, 11, 11, 11, 11, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 4, 11, 11, 31, 31, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/205 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1cccc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526904269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526904269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001526904269 none O=C(Nc1ccnn1Cc1cccc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 11, 11, 11, 11, 11, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 4, 11, 11, 31, 31, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526904269 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 Building ZINC001526904269 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526904269 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 204) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1cccc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526904269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526904269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001526904269 none O=C(Nc1ccnn1Cc1cccc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 11, 11, 11, 11, 11, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 4, 11, 11, 31, 31, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 205) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1cccc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001526904269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526904269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001526904269 none O=C(Nc1ccnn1Cc1cccc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 11, 11, 11, 11, 11, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 4, 11, 11, 31, 31, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526904269 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526904269 Building ZINC001526926033 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526926033 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/206 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n(c2ccc(C)cc2)n1) `ZINC001526926033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526926033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001526926033 none COc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n(c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 48, 48, 12, 12, 12, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 48, 48, 48, 48, 12, 7, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/207 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n(c2ccc(C)cc2)n1) `ZINC001526926033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526926033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001526926033 none COc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n(c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 48, 48, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 48, 48, 48, 48, 10, 5, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526926033 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 Building ZINC001526926033 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526926033 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 206) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n(c2ccc(C)cc2)n1) `ZINC001526926033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526926033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001526926033 none COc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n(c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 48, 48, 12, 12, 12, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 48, 48, 48, 48, 12, 7, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 207) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n(c2ccc(C)cc2)n1) `ZINC001526926033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526926033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001526926033 none COc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n(c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 48, 48, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 48, 48, 48, 48, 10, 5, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526926033 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526926033 Building ZINC001526928512 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526928512 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/208 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(Cc2ccccc2Br)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526928512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526928512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001526928512 none O=C(NC1(Cc2ccccc2Br)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 8, 23, 39, 39, 32, 39, 39, 39, 8, 8, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 23, 23, 39, 39, 39, 39, 8, 8, 8, 8, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/209 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(Cc2ccccc2Br)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526928512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526928512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001526928512 none O=C(NC1(Cc2ccccc2Br)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 8, 23, 40, 40, 31, 40, 40, 40, 8, 8, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 23, 23, 40, 40, 40, 40, 8, 8, 8, 8, 5, 1, 5] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526928512 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 Building ZINC001526928512 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526928512 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 208) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(Cc2ccccc2Br)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526928512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526928512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001526928512 none O=C(NC1(Cc2ccccc2Br)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 8, 23, 39, 39, 32, 39, 39, 39, 8, 8, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 23, 23, 39, 39, 39, 39, 8, 8, 8, 8, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 209) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(Cc2ccccc2Br)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526928512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526928512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001526928512 none O=C(NC1(Cc2ccccc2Br)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 8, 23, 40, 40, 31, 40, 40, 40, 8, 8, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 23, 23, 40, 40, 40, 40, 8, 8, 8, 8, 5, 1, 5] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526928512 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526928512 Building ZINC001526933682 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526933682 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/210 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)n(c3cccc(C)c3)n2)cc1) `ZINC001526933682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526933682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001526933682 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 11, 11, 11, 11, 11, 11, 7, 14, 14, 14, 14, 14, 14, 14, 7, 4, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/211 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)n(c3cccc(C)c3)n2)cc1) `ZINC001526933682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526933682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001526933682 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 14, 14, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 11, 11, 7, 11, 11, 11, 7, 14, 14, 14, 14, 14, 14, 14, 7, 4, 5, 5, 5, 5, 5, 5, 5, 11, 11, 7, 11, 11, 11, 11, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526933682 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 Building ZINC001526933682 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526933682 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 210) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)n(c3cccc(C)c3)n2)cc1) `ZINC001526933682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526933682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001526933682 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 11, 11, 11, 11, 11, 11, 7, 14, 14, 14, 14, 14, 14, 14, 7, 4, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 211) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)n(c3cccc(C)c3)n2)cc1) `ZINC001526933682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526933682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001526933682 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 14, 14, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 11, 11, 7, 11, 11, 11, 7, 14, 14, 14, 14, 14, 14, 14, 7, 4, 5, 5, 5, 5, 5, 5, 5, 11, 11, 7, 11, 11, 11, 11, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526933682 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933682 Building ZINC001526933881 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526933881 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/212 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)n(c3cccc(C)c3)n2)cc1) `ZINC001526933881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526933881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001526933881 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 21, 21, 20, 21, 21, 21, 10, 26, 26, 26, 26, 26, 26, 26, 10, 6, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 26, 26] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/213 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)n(c3cccc(C)c3)n2)cc1) `ZINC001526933881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526933881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001526933881 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 27, 27, 11, 11, 11, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 21, 21, 21, 21, 21, 21, 11, 27, 27, 27, 27, 27, 27, 27, 11, 7, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526933881 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 Building ZINC001526933881 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526933881 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 212) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)n(c3cccc(C)c3)n2)cc1) `ZINC001526933881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526933881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001526933881 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 21, 21, 20, 21, 21, 21, 10, 26, 26, 26, 26, 26, 26, 26, 10, 6, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 26, 26] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 213) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)n(c3cccc(C)c3)n2)cc1) `ZINC001526933881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526933881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001526933881 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 27, 27, 11, 11, 11, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 21, 21, 21, 21, 21, 21, 11, 27, 27, 27, 27, 27, 27, 27, 11, 7, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526933881 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526933881 Building ZINC001526945615 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526945615 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/214 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 34, 48, 48, 34, 48, 48, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 48, 48, 41, 48, 48, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/215 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 34, 48, 48, 34, 48, 48, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 48, 48, 41, 48, 48, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/216 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/216' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 38, 48, 48, 38, 48, 48, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 38, 38, 48, 48, 38, 48, 48, 15, 15, 15, 15, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/217 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/217' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 38, 48, 48, 38, 48, 48, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 38, 38, 48, 48, 38, 48, 48, 15, 15, 15, 15, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526945615 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 Building ZINC001526945615 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526945615 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 214) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 34, 48, 48, 34, 48, 48, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 48, 48, 41, 48, 48, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 215) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 34, 48, 48, 34, 48, 48, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 48, 48, 41, 48, 48, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 216) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 38, 48, 48, 38, 48, 48, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 38, 38, 48, 48, 38, 48, 48, 15, 15, 15, 15, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 217) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 38, 48, 48, 38, 48, 48, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 38, 38, 48, 48, 38, 48, 48, 15, 15, 15, 15, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526945615 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 Building ZINC001526945615 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526945615 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 214) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 34, 48, 48, 34, 48, 48, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 48, 48, 41, 48, 48, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 215) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 34, 48, 48, 34, 48, 48, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 48, 48, 41, 48, 48, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 216) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 38, 48, 48, 38, 48, 48, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 38, 38, 48, 48, 38, 48, 48, 15, 15, 15, 15, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 217) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 38, 48, 48, 38, 48, 48, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 38, 38, 48, 48, 38, 48, 48, 15, 15, 15, 15, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526945615 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 Building ZINC001526945615 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526945615 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 214) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 34, 48, 48, 34, 48, 48, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 48, 48, 41, 48, 48, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 215) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 34, 48, 48, 34, 48, 48, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 34, 34, 48, 48, 41, 48, 48, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 216) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 38, 48, 48, 38, 48, 48, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 38, 38, 48, 48, 38, 48, 48, 15, 15, 15, 15, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 217) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001526945615.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526945615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001526945615 none O=C(N1CCC2(C1)CCN(Cc1ccccc1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 38, 48, 48, 38, 48, 48, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 38, 38, 48, 48, 38, 48, 48, 15, 15, 15, 15, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526945615 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526945615 Building ZINC001526998747 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526998747 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/218 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001526998747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526998747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001526998747 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 28, 28, 22, 28, 28, 16, 16, 9, 6, 9, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 9, 9, 9, 9, 16, 16, 16, 28, 28, 24, 28, 28, 16, 16, 16, 6, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/219 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001526998747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526998747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001526998747 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 30, 30, 25, 30, 30, 16, 16, 8, 5, 8, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 8, 16, 16, 16, 30, 30, 26, 30, 30, 16, 16, 16, 5, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526998747 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 Building ZINC001526998747 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526998747 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 218) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001526998747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526998747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001526998747 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 28, 28, 22, 28, 28, 16, 16, 9, 6, 9, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 9, 9, 9, 9, 16, 16, 16, 28, 28, 24, 28, 28, 16, 16, 16, 6, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 219) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001526998747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526998747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001526998747 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 30, 30, 25, 30, 30, 16, 16, 8, 5, 8, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 8, 16, 16, 16, 30, 30, 26, 30, 30, 16, 16, 16, 5, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526998747 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998747 Building ZINC001526998750 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526998750 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/220 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001526998750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526998750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001526998750 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 30, 30, 16, 30, 30, 16, 16, 8, 5, 8, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 8, 16, 16, 16, 30, 30, 16, 30, 30, 16, 16, 16, 5, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/221 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001526998750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526998750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001526998750 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 31, 31, 17, 31, 31, 17, 17, 9, 6, 9, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 9, 9, 9, 9, 17, 17, 17, 31, 31, 17, 31, 31, 17, 17, 17, 6, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526998750 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 Building ZINC001526998750 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526998750 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 220) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001526998750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526998750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001526998750 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 30, 30, 16, 30, 30, 16, 16, 8, 5, 8, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 8, 16, 16, 16, 30, 30, 16, 30, 30, 16, 16, 16, 5, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 221) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001526998750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526998750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001526998750 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 31, 31, 17, 31, 31, 17, 17, 9, 6, 9, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 9, 9, 9, 9, 17, 17, 17, 31, 31, 17, 31, 31, 17, 17, 17, 6, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001526998750 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001526998750 Building ZINC001527013420 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527013420 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/222 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527013420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527013420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527013420 none Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 3, 34, 33, 37, 37, 36, 37, 37, 37, 36, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 36, 37, 36, 37, 36, 36, 37, 36, 37, 36, 36, 7, 7, 3, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/223 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527013420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527013420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527013420 none Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 6, 8, 33, 33, 38, 38, 38, 38, 38, 38, 38, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8, 3, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527013420 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 Building ZINC001527013420 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527013420 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 222) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527013420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527013420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527013420 none Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 3, 34, 33, 37, 37, 36, 37, 37, 37, 36, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 36, 37, 36, 37, 36, 36, 37, 36, 37, 36, 36, 7, 7, 3, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 223) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527013420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527013420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527013420 none Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 6, 8, 33, 33, 38, 38, 38, 38, 38, 38, 38, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8, 3, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527013420 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013420 Building ZINC001527013421 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527013421 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/224 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527013421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527013421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527013421 none Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 5, 31, 31, 37, 37, 37, 37, 37, 37, 37, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 3, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/225 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527013421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527013421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527013421 none Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 2, 8, 32, 32, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 35, 6, 6, 2, 7, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527013421 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 Building ZINC001527013421 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527013421 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 224) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527013421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527013421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527013421 none Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 5, 31, 31, 37, 37, 37, 37, 37, 37, 37, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 3, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 225) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527013421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527013421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527013421 none Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 2, 8, 32, 32, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 35, 6, 6, 2, 7, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527013421 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527013421 Building ZINC001527079632 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527079632 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/226 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cccc1C(=O)Nc1ccccc1) `ZINC001527079632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527079632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527079632 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cccc1C(=O)Nc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 31, 31, 31, 42, 42, 31, 42, 42, 8, 8, 8, 2, 7, 7, 8, 8, 8, 31, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/227 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cccc1C(=O)Nc1ccccc1) `ZINC001527079632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527079632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527079632 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cccc1C(=O)Nc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 26, 26, 26, 40, 40, 26, 40, 40, 8, 8, 8, 2, 6, 6, 8, 8, 8, 26, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527079632 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 Building ZINC001527079632 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527079632 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 226) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cccc1C(=O)Nc1ccccc1) `ZINC001527079632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527079632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527079632 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cccc1C(=O)Nc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 31, 31, 31, 42, 42, 31, 42, 42, 8, 8, 8, 2, 7, 7, 8, 8, 8, 31, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 227) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cccc1C(=O)Nc1ccccc1) `ZINC001527079632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527079632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527079632 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cccc1C(=O)Nc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 26, 26, 26, 40, 40, 26, 40, 40, 8, 8, 8, 2, 6, 6, 8, 8, 8, 26, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527079632 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527079632 Building ZINC001527110422 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527110422 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/228 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@@H]2C)cc1OC) `ZINC001527110422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527110422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110422 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 10, 10, 10, 3, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 23, 21, 21, 21, 10, 10, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 23, 23, 23] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 73 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/229 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@@H]2C)cc1OC) `ZINC001527110422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527110422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110422 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 10, 10, 10, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 24, 24, 24, 24, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527110422 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 Building ZINC001527110422 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527110422 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 228) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@@H]2C)cc1OC) `ZINC001527110422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527110422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110422 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 10, 10, 10, 3, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 23, 21, 21, 21, 10, 10, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 23, 23, 23] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 73 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 229) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@@H]2C)cc1OC) `ZINC001527110422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527110422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110422 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 10, 10, 10, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 24, 24, 24, 24, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527110422 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110422 Building ZINC001527110439 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527110439 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/230 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@H]2C)cc1OC) `ZINC001527110439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527110439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110439 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 10, 10, 10, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 24, 24, 24, 24, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/231 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@H]2C)cc1OC) `ZINC001527110439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527110439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110439 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 4, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 25, 23, 23, 23, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 77 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527110439 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 Building ZINC001527110439 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527110439 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 230) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@H]2C)cc1OC) `ZINC001527110439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527110439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110439 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 10, 10, 10, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 24, 24, 24, 24, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 24, 24, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 231) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@H]2C)cc1OC) `ZINC001527110439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527110439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110439 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 4, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 25, 23, 23, 23, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 77 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527110439 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110439 Building ZINC001527110441 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527110441 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/232 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@@H]2C)cc1OC) `ZINC001527110441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527110441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110441 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 16, 16, 16, 8, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 28, 27, 27, 27, 16, 16, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 28, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/233 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@@H]2C)cc1OC) `ZINC001527110441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527110441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110441 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 12, 12, 12, 5, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 27, 27, 27, 27, 12, 12, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527110441 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 Building ZINC001527110441 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527110441 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 232) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@@H]2C)cc1OC) `ZINC001527110441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527110441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110441 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 16, 16, 16, 8, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 28, 27, 27, 27, 16, 16, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 28, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 233) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@@H]2C)cc1OC) `ZINC001527110441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527110441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110441 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 12, 12, 12, 5, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 27, 27, 27, 27, 12, 12, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527110441 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110441 Building ZINC001527110443 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527110443 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/234 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@H]2C)cc1OC) `ZINC001527110443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527110443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110443 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 25, 25, 25, 25, 13, 13, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/235 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@H]2C)cc1OC) `ZINC001527110443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527110443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110443 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 8, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 25, 25, 25, 25, 14, 14, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527110443 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 Building ZINC001527110443 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527110443 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 234) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@H]2C)cc1OC) `ZINC001527110443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527110443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110443 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 25, 25, 25, 25, 13, 13, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 235) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@H]2C)cc1OC) `ZINC001527110443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527110443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001527110443 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 8, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 25, 25, 25, 25, 14, 14, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527110443 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527110443 Building ZINC001527121608 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527121608 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/236 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/236' -> `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)NCc1ccc(Oc2ccc(Cl)cc2Cl)c(C)c1) `ZINC001527121608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527121608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001527121608 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(Cl)cc2Cl)c(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 39, 39, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 39, 39, 50, 50, 50, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/237 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/237' -> `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)NCc1ccc(Oc2ccc(Cl)cc2Cl)c(C)c1) `ZINC001527121608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527121608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001527121608 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(Cl)cc2Cl)c(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 39, 39, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 39, 39, 50, 50, 50, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527121608 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608 Building ZINC001527121608 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527121608 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 236) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc1ccc(Oc2ccc(Cl)cc2Cl)c(C)c1) `ZINC001527121608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527121608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001527121608 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(Cl)cc2Cl)c(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 39, 39, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 39, 39, 50, 50, 50, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 237) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc1ccc(Oc2ccc(Cl)cc2Cl)c(C)c1) `ZINC001527121608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527121608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001527121608 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(Cl)cc2Cl)c(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 39, 39, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 39, 39, 50, 50, 50, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/150923/xbj-8058088.36/working/building/ZINC001527121608 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527121608 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527121608 Building ZINC001527158666 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527158666 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/238 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(C(F)(F)F)c1) `ZINC001527158666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527158666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527158666 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 10, 12, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 2, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/239 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(C(F)(F)F)c1) `ZINC001527158666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527158666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527158666 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 11, 13, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 3, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 90 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527158666 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 Building ZINC001527158666 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527158666 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 238) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(C(F)(F)F)c1) `ZINC001527158666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527158666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527158666 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 10, 12, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 2, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 239) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(C(F)(F)F)c1) `ZINC001527158666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527158666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527158666 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 11, 13, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 3, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 90 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527158666 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527158666 Building ZINC001527161136 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527161136 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/240 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc2[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527161136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527161136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527161136 none O=C(N1CCc2ccccc2[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 10, 10] 37 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/241 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc2[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527161136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527161136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527161136 none O=C(N1CCc2ccccc2[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 19, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 19, 25, 25, 12, 12] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527161136 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 Building ZINC001527161136 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527161136 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 240) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc2[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527161136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527161136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527161136 none O=C(N1CCc2ccccc2[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 10, 10] 37 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 241) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc2[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527161136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527161136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527161136 none O=C(N1CCc2ccccc2[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 19, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 19, 25, 25, 12, 12] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527161136 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527161136 Building ZINC001527219340 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527219340 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/242 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527219340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219340 none CC(C)(C)OC(=O)[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 39, 11, 39, 11, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 3, 3, 1, 3, 11, 11, 11, 11] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/243 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527219340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219340 none CC(C)(C)OC(=O)[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 39, 11, 39, 11, 11, 11, 7, 11, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 42, 42, 42, 42, 42, 42, 42, 42, 42, 11, 11, 4, 3, 1, 3, 11, 11, 11, 11] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527219340 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 Building ZINC001527219340 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527219340 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 242) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527219340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219340 none CC(C)(C)OC(=O)[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 39, 11, 39, 11, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 3, 3, 1, 3, 11, 11, 11, 11] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 243) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527219340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219340 none CC(C)(C)OC(=O)[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 39, 11, 39, 11, 11, 11, 7, 11, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 42, 42, 42, 42, 42, 42, 42, 42, 42, 11, 11, 4, 3, 1, 3, 11, 11, 11, 11] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527219340 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219340 Building ZINC001527219342 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527219342 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/244 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527219342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219342 none CC(C)(C)OC(=O)[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 44, 9, 44, 9, 9, 9, 6, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 9, 9, 4, 3, 1, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/245 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527219342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219342 none CC(C)(C)OC(=O)[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 9, 45, 9, 9, 9, 6, 9, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 9, 9, 3, 3, 1, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527219342 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 Building ZINC001527219342 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527219342 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 244) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527219342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219342 none CC(C)(C)OC(=O)[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 44, 9, 44, 9, 9, 9, 6, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 9, 9, 4, 3, 1, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 245) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527219342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219342 none CC(C)(C)OC(=O)[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 9, 45, 9, 9, 9, 6, 9, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 9, 9, 3, 3, 1, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527219342 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219342 Building ZINC001527219344 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527219344 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/246 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527219344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219344 none CC(C)(C)OC(=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 9, 44, 9, 9, 9, 6, 9, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 9, 9, 3, 3, 1, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/247 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527219344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219344 none CC(C)(C)OC(=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 42, 9, 42, 9, 9, 9, 6, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 9, 9, 4, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527219344 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 Building ZINC001527219344 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527219344 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 246) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527219344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219344 none CC(C)(C)OC(=O)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 9, 44, 9, 9, 9, 6, 9, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 9, 9, 3, 3, 1, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 247) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527219344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219344 none CC(C)(C)OC(=O)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 42, 9, 42, 9, 9, 9, 6, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 9, 9, 4, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527219344 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219344 Building ZINC001527219346 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527219346 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/248 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527219346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219346 none CC(C)(C)OC(=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 39, 11, 39, 11, 11, 11, 7, 11, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 4, 3, 3, 3, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/249 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527219346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219346 none CC(C)(C)OC(=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 39, 11, 39, 11, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 3, 3, 1, 3, 11, 11, 11, 11] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527219346 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 Building ZINC001527219346 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527219346 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 248) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527219346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219346 none CC(C)(C)OC(=O)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 39, 11, 39, 11, 11, 11, 7, 11, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 4, 3, 3, 3, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 249) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001527219346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527219346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001527219346 none CC(C)(C)OC(=O)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 39, 11, 39, 11, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 3, 3, 1, 3, 11, 11, 11, 11] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527219346 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527219346 Building ZINC001527223642 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527223642 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/250 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)c(F)cc1N1CCCCC1) `ZINC001527223642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527223642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001527223642 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)c(F)cc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 10, 13, 13, 13, 18, 30, 30, 30, 30, 30, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 6, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/251 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)c(F)cc1N1CCCCC1) `ZINC001527223642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527223642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001527223642 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)c(F)cc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 8, 13, 13, 13, 18, 30, 30, 30, 30, 30, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4, 6, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527223642 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 Building ZINC001527223642 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527223642 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 250) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)c(F)cc1N1CCCCC1) `ZINC001527223642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527223642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001527223642 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)c(F)cc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 10, 13, 13, 13, 18, 30, 30, 30, 30, 30, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 6, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 251) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)c(F)cc1N1CCCCC1) `ZINC001527223642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527223642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001527223642 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)c(F)cc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 8, 13, 13, 13, 18, 30, 30, 30, 30, 30, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4, 6, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527223642 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527223642 Building ZINC001527224584 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527224584 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/252 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2) `ZINC001527224584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527224584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001527224584 none CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 43, 6, 6, 6, 6, 6, 6, 6, 3, 6, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 6, 6, 6, 3, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/253 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2) `ZINC001527224584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527224584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001527224584 none CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 31, 42, 9, 9, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 9, 9, 9, 4, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527224584 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 Building ZINC001527224584 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527224584 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 252) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2) `ZINC001527224584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527224584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001527224584 none CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 43, 6, 6, 6, 6, 6, 6, 6, 3, 6, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 6, 6, 6, 3, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 253) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2) `ZINC001527224584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527224584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001527224584 none CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 31, 42, 9, 9, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 9, 9, 9, 4, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527224584 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224584 Building ZINC001527224585 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527224585 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/254 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2) `ZINC001527224585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527224585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001527224585 none CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 43, 9, 9, 9, 9, 9, 9, 9, 7, 9, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 9, 9, 4, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/255 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2) `ZINC001527224585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527224585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001527224585 none CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 31, 42, 6, 6, 6, 6, 6, 6, 6, 5, 6, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 6, 6, 6, 3, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527224585 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 Building ZINC001527224585 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527224585 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 254) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2) `ZINC001527224585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527224585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001527224585 none CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 43, 9, 9, 9, 9, 9, 9, 9, 7, 9, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 9, 9, 4, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 255) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2) `ZINC001527224585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527224585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001527224585 none CC(C)(C)OC(=O)Nc1ccc2c(c1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CC(C)(C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 31, 42, 6, 6, 6, 6, 6, 6, 6, 5, 6, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 6, 6, 6, 3, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527224585 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527224585 Building ZINC001527231888 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231888 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/256 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 33, 39, 39, 33, 33, 39, 39, 8, 8, 8, 8, 13, 13, 13, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 33, 33, 39, 39, 39, 39, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/257 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 36, 40, 40, 36, 37, 40, 40, 8, 8, 8, 8, 12, 12, 12, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 36, 36, 40, 40, 40, 40, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/258 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/258' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 33, 39, 39, 33, 33, 39, 39, 8, 8, 8, 8, 13, 13, 13, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 33, 33, 39, 39, 39, 39, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/259 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/259' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 36, 40, 40, 36, 37, 40, 40, 8, 8, 8, 8, 12, 12, 12, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 36, 36, 40, 40, 40, 40, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231888 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 Building ZINC001527231888 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231888 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 256) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 33, 39, 39, 33, 33, 39, 39, 8, 8, 8, 8, 13, 13, 13, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 33, 33, 39, 39, 39, 39, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 257) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 36, 40, 40, 36, 37, 40, 40, 8, 8, 8, 8, 12, 12, 12, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 36, 36, 40, 40, 40, 40, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 258) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 33, 39, 39, 33, 33, 39, 39, 8, 8, 8, 8, 13, 13, 13, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 33, 33, 39, 39, 39, 39, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 259) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 36, 40, 40, 36, 37, 40, 40, 8, 8, 8, 8, 12, 12, 12, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 36, 36, 40, 40, 40, 40, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231888 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 Building ZINC001527231888 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231888 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 256) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 33, 39, 39, 33, 33, 39, 39, 8, 8, 8, 8, 13, 13, 13, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 33, 33, 39, 39, 39, 39, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 257) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 36, 40, 40, 36, 37, 40, 40, 8, 8, 8, 8, 12, 12, 12, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 36, 36, 40, 40, 40, 40, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 258) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 33, 39, 39, 33, 33, 39, 39, 8, 8, 8, 8, 13, 13, 13, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 33, 33, 39, 39, 39, 39, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 259) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 36, 40, 40, 36, 37, 40, 40, 8, 8, 8, 8, 12, 12, 12, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 36, 36, 40, 40, 40, 40, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231888 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 Building ZINC001527231888 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231888 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 256) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 33, 39, 39, 33, 33, 39, 39, 8, 8, 8, 8, 13, 13, 13, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 33, 33, 39, 39, 39, 39, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 257) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 36, 40, 40, 36, 37, 40, 40, 8, 8, 8, 8, 12, 12, 12, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 36, 36, 40, 40, 40, 40, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 258) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 33, 39, 39, 33, 33, 39, 39, 8, 8, 8, 8, 13, 13, 13, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 33, 33, 39, 39, 39, 39, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 259) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C) `ZINC001527231888.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231888 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 36, 40, 40, 36, 37, 40, 40, 8, 8, 8, 8, 12, 12, 12, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 36, 36, 40, 40, 40, 40, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231888 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231888 Building ZINC001527231889 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231889 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/260 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 16, 18, 18, 18, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/261 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 18, 18, 18, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/262 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/262' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 16, 18, 18, 18, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/263 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/263' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 18, 18, 18, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231889 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 Building ZINC001527231889 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231889 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 260) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 16, 18, 18, 18, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 261) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 18, 18, 18, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 262) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 16, 18, 18, 18, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 263) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 18, 18, 18, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231889 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 Building ZINC001527231889 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231889 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 260) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 16, 18, 18, 18, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 261) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 18, 18, 18, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 262) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 16, 18, 18, 18, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 263) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 18, 18, 18, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231889 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 Building ZINC001527231889 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231889 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 260) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 16, 18, 18, 18, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 261) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 18, 18, 18, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 262) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 16, 18, 18, 18, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 263) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C) `ZINC001527231889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001527231889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(Cl)cc2)C[C@H]1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 18, 18, 18, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231889 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231889 Building ZINC001527231915 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231915 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/264 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 8, 8, 8, 8, 8, 8, 36, 47, 47, 36, 43, 47, 47, 8, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 36, 36, 47, 47, 47, 47, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/265 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 8, 8, 8, 8, 8, 8, 36, 47, 47, 36, 43, 47, 47, 8, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 36, 36, 47, 47, 47, 47, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/266 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/266' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 8, 8, 8, 8, 33, 34, 34, 33, 33, 34, 34, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 33, 33, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 3, 3] 38 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/267 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/267' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 8, 8, 8, 8, 33, 34, 34, 33, 33, 34, 34, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 33, 33, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 3, 3] 38 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231915 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 Building ZINC001527231915 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231915 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 264) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 8, 8, 8, 8, 8, 8, 36, 47, 47, 36, 43, 47, 47, 8, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 36, 36, 47, 47, 47, 47, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 265) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 8, 8, 8, 8, 8, 8, 36, 47, 47, 36, 43, 47, 47, 8, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 36, 36, 47, 47, 47, 47, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 266) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 8, 8, 8, 8, 33, 34, 34, 33, 33, 34, 34, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 33, 33, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 3, 3] 38 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 267) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 8, 8, 8, 8, 33, 34, 34, 33, 33, 34, 34, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 33, 33, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 3, 3] 38 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231915 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 Building ZINC001527231915 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231915 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 264) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 8, 8, 8, 8, 8, 8, 36, 47, 47, 36, 43, 47, 47, 8, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 36, 36, 47, 47, 47, 47, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 265) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 8, 8, 8, 8, 8, 8, 36, 47, 47, 36, 43, 47, 47, 8, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 36, 36, 47, 47, 47, 47, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 266) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 8, 8, 8, 8, 33, 34, 34, 33, 33, 34, 34, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 33, 33, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 3, 3] 38 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 267) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 8, 8, 8, 8, 33, 34, 34, 33, 33, 34, 34, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 33, 33, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 3, 3] 38 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231915 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 Building ZINC001527231915 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231915 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 264) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 8, 8, 8, 8, 8, 8, 36, 47, 47, 36, 43, 47, 47, 8, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 36, 36, 47, 47, 47, 47, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 265) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 8, 8, 8, 8, 8, 8, 36, 47, 47, 36, 43, 47, 47, 8, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 36, 36, 47, 47, 47, 47, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 266) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 8, 8, 8, 8, 33, 34, 34, 33, 33, 34, 34, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 33, 33, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 3, 3] 38 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 267) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231915 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 8, 8, 8, 8, 33, 34, 34, 33, 33, 34, 34, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 33, 33, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 3, 3] 38 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231915 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231915 Building ZINC001527231916 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231916 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/268 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 19, 19, 19, 19, 49, 50, 50, 49, 49, 50, 50, 19, 19, 16, 2, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/269 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 19, 19, 19, 19, 49, 50, 50, 49, 49, 50, 50, 19, 19, 16, 2, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/270 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/270' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 49, 50, 50, 49, 49, 50, 50, 20, 20, 17, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 49, 49, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/271 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/271' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 49, 50, 50, 49, 49, 50, 50, 20, 20, 17, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 49, 49, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231916 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 Building ZINC001527231916 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231916 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 268) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 19, 19, 19, 19, 49, 50, 50, 49, 49, 50, 50, 19, 19, 16, 2, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 269) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 19, 19, 19, 19, 49, 50, 50, 49, 49, 50, 50, 19, 19, 16, 2, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 270) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 49, 50, 50, 49, 49, 50, 50, 20, 20, 17, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 49, 49, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 271) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 49, 50, 50, 49, 49, 50, 50, 20, 20, 17, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 49, 49, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231916 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 Building ZINC001527231916 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231916 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 268) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 19, 19, 19, 19, 49, 50, 50, 49, 49, 50, 50, 19, 19, 16, 2, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 269) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 19, 19, 19, 19, 49, 50, 50, 49, 49, 50, 50, 19, 19, 16, 2, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 270) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 49, 50, 50, 49, 49, 50, 50, 20, 20, 17, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 49, 49, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 271) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 49, 50, 50, 49, 49, 50, 50, 20, 20, 17, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 49, 49, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231916 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 Building ZINC001527231916 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001527231916 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 268) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 19, 19, 19, 19, 49, 50, 50, 49, 49, 50, 50, 19, 19, 16, 2, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 269) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 19, 19, 19, 19, 49, 50, 50, 49, 49, 50, 50, 19, 19, 16, 2, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 270) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 49, 50, 50, 49, 49, 50, 50, 20, 20, 17, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 49, 49, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 271) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001527231916.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001527231916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001527231916 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 49, 50, 50, 49, 49, 50, 50, 20, 20, 17, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 49, 49, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527231916 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527231916 Building ZINC001527239692 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527239692 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/272 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2c3cccc(Br)c3CC2(C)C)cc1Cl) `ZINC001527239692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527239692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527239692 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2c3cccc(Br)c3CC2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 13, 13, 13, 6, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/273 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2c3cccc(Br)c3CC2(C)C)cc1Cl) `ZINC001527239692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527239692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527239692 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2c3cccc(Br)c3CC2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527239692 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 Building ZINC001527239692 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527239692 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 272) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2c3cccc(Br)c3CC2(C)C)cc1Cl) `ZINC001527239692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527239692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527239692 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2c3cccc(Br)c3CC2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 13, 13, 13, 6, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 273) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2c3cccc(Br)c3CC2(C)C)cc1Cl) `ZINC001527239692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527239692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527239692 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2c3cccc(Br)c3CC2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527239692 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239692 Building ZINC001527239693 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527239693 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/274 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2c3cccc(Br)c3CC2(C)C)cc1Cl) `ZINC001527239693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527239693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527239693 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2c3cccc(Br)c3CC2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/275 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2c3cccc(Br)c3CC2(C)C)cc1Cl) `ZINC001527239693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527239693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527239693 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2c3cccc(Br)c3CC2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527239693 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 Building ZINC001527239693 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527239693 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 274) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2c3cccc(Br)c3CC2(C)C)cc1Cl) `ZINC001527239693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527239693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527239693 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2c3cccc(Br)c3CC2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 275) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2c3cccc(Br)c3CC2(C)C)cc1Cl) `ZINC001527239693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527239693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527239693 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2c3cccc(Br)c3CC2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527239693 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527239693 Building ZINC001527258019 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527258019 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/276 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnn(c3ccc(F)cc3)c2C(F)(F)F)cc1Cl) `ZINC001527258019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527258019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527258019 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnn(c3ccc(F)cc3)c2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 4, 8, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/277 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnn(c3ccc(F)cc3)c2C(F)(F)F)cc1Cl) `ZINC001527258019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527258019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527258019 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnn(c3ccc(F)cc3)c2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 6, 6, 6, 14, 14, 14, 6, 6, 4, 9, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527258019 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 Building ZINC001527258019 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527258019 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 276) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnn(c3ccc(F)cc3)c2C(F)(F)F)cc1Cl) `ZINC001527258019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527258019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527258019 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnn(c3ccc(F)cc3)c2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 4, 8, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 277) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnn(c3ccc(F)cc3)c2C(F)(F)F)cc1Cl) `ZINC001527258019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527258019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527258019 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnn(c3ccc(F)cc3)c2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 6, 6, 6, 14, 14, 14, 6, 6, 4, 9, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527258019 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527258019 Building ZINC001527275420 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527275420 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/278 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC001527275420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527275420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001527275420 none CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 23, 29, 10, 4, 3, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 10, 10, 4, 4, 3, 3, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/279 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC001527275420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527275420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001527275420 none CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 22, 28, 10, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 22, 10, 10, 4, 4, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 10, 11, 12, 13, 14, 15, 16, 49, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527275420 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 Building ZINC001527275420 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527275420 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 278) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC001527275420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527275420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001527275420 none CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 23, 29, 10, 4, 3, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 10, 10, 4, 4, 3, 3, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 279) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC001527275420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527275420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001527275420 none CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 22, 28, 10, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 22, 10, 10, 4, 4, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 10, 11, 12, 13, 14, 15, 16, 49, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527275420 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275420 Building ZINC001527275421 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527275421 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/280 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC001527275421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527275421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001527275421 none CC(C)(C)OC(=O)NCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 24, 30, 10, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 10, 10, 4, 4, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [17, 10, 11, 12, 13, 14, 15, 16, 49, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/281 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC001527275421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527275421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001527275421 none CC(C)(C)OC(=O)NCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 22, 28, 10, 4, 3, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 22, 10, 10, 4, 4, 3, 3, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527275421 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 Building ZINC001527275421 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527275421 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 280) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC001527275421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527275421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001527275421 none CC(C)(C)OC(=O)NCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 24, 30, 10, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 10, 10, 4, 4, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2] 50 rigid atoms, others: [17, 10, 11, 12, 13, 14, 15, 16, 49, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 281) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC001527275421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527275421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001527275421 none CC(C)(C)OC(=O)NCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 22, 28, 10, 4, 3, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 22, 10, 10, 4, 4, 3, 3, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527275421 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527275421 Building ZINC001527312655 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527312655 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/282 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc(Br)cc2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527312655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527312655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001527312655 none O=C(NC1(c2ccc(Br)cc2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 12, 18, 27, 27, 26, 26, 27, 27, 18, 18, 18, 1, 1, 1, 12, 12, 12, 12, 12, 6, 27, 27, 27, 27, 18, 18, 18, 18, 18, 18, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/283 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc(Br)cc2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527312655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527312655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001527312655 none O=C(NC1(c2ccc(Br)cc2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 17, 26, 26, 21, 21, 26, 26, 17, 17, 17, 1, 1, 1, 12, 12, 12, 12, 12, 6, 26, 26, 26, 26, 17, 17, 17, 17, 17, 17, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527312655 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 Building ZINC001527312655 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527312655 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 282) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc(Br)cc2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527312655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527312655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001527312655 none O=C(NC1(c2ccc(Br)cc2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 12, 18, 27, 27, 26, 26, 27, 27, 18, 18, 18, 1, 1, 1, 12, 12, 12, 12, 12, 6, 27, 27, 27, 27, 18, 18, 18, 18, 18, 18, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 283) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc(Br)cc2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527312655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527312655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001527312655 none O=C(NC1(c2ccc(Br)cc2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 17, 26, 26, 21, 21, 26, 26, 17, 17, 17, 1, 1, 1, 12, 12, 12, 12, 12, 6, 26, 26, 26, 26, 17, 17, 17, 17, 17, 17, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527312655 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527312655 Building ZINC001527329799 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527329799 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/284 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br) `ZINC001527329799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527329799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001527329799 none Cc1cc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 32, 32, 24, 31, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 4, 6, 6, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/285 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br) `ZINC001527329799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527329799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001527329799 none Cc1cc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 32, 32, 22, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 4, 6, 6, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527329799 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 Building ZINC001527329799 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527329799 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 284) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br) `ZINC001527329799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527329799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001527329799 none Cc1cc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 32, 32, 24, 31, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 4, 6, 6, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 285) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br) `ZINC001527329799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527329799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001527329799 none Cc1cc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 32, 32, 22, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 4, 6, 6, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527329799 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527329799 Building ZINC001527421951 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527421951 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/286 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(C)cc2C)CCCC1) `ZINC001527421951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527421951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527421951 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(C)cc2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 126 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/287 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(C)cc2C)CCCC1) `ZINC001527421951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527421951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527421951 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(C)cc2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 4, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 4, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527421951 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 Building ZINC001527421951 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527421951 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 286) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(C)cc2C)CCCC1) `ZINC001527421951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527421951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527421951 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(C)cc2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 126 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 287) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(C)cc2C)CCCC1) `ZINC001527421951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527421951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527421951 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(C)cc2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 4, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 4, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527421951 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527421951 Building ZINC001527422071 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527422071 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/288 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(Cc2ccc(F)cc2Cl)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001527422071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527422071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527422071 none O=C(NC1(Cc2ccc(F)cc2Cl)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 35, 42, 42, 37, 38, 42, 42, 42, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 35, 35, 42, 42, 42, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/289 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(Cc2ccc(F)cc2Cl)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001527422071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527422071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527422071 none O=C(NC1(Cc2ccc(F)cc2Cl)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 35, 42, 42, 37, 42, 42, 42, 42, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 35, 35, 42, 42, 42, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527422071 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 Building ZINC001527422071 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527422071 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 288) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(Cc2ccc(F)cc2Cl)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001527422071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527422071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527422071 none O=C(NC1(Cc2ccc(F)cc2Cl)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 35, 42, 42, 37, 38, 42, 42, 42, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 35, 35, 42, 42, 42, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 289) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(Cc2ccc(F)cc2Cl)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001527422071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527422071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001527422071 none O=C(NC1(Cc2ccc(F)cc2Cl)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 35, 42, 42, 37, 42, 42, 42, 42, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 35, 35, 42, 42, 42, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527422071 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527422071 Building ZINC001527441549 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527441549 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/290 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(F)cc1) `ZINC001527441549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527441549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527441549 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/291 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(F)cc1) `ZINC001527441549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527441549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527441549 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527441549 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 Building ZINC001527441549 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527441549 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 290) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(F)cc1) `ZINC001527441549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527441549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527441549 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 291) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(F)cc1) `ZINC001527441549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527441549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527441549 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527441549 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441549 Building ZINC001527441552 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527441552 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/292 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(F)cc1) `ZINC001527441552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527441552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527441552 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/293 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(F)cc1) `ZINC001527441552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527441552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527441552 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527441552 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 Building ZINC001527441552 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527441552 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 292) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(F)cc1) `ZINC001527441552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527441552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527441552 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 293) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(F)cc1) `ZINC001527441552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527441552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527441552 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527441552 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527441552 Building ZINC001527532308 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527532308 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/294 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1c(Cl)cccc1Cl) `ZINC001527532308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527532308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001527532308 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 17, 17, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/295 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1c(Cl)cccc1Cl) `ZINC001527532308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527532308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001527532308 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 16, 16, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527532308 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 Building ZINC001527532308 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527532308 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 294) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1c(Cl)cccc1Cl) `ZINC001527532308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527532308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001527532308 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 17, 17, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 295) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1c(Cl)cccc1Cl) `ZINC001527532308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527532308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001527532308 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 16, 16, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527532308 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532308 Building ZINC001527532309 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527532309 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/296 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1c(Cl)cccc1Cl) `ZINC001527532309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527532309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001527532309 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 3, 16, 16, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/297 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1c(Cl)cccc1Cl) `ZINC001527532309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527532309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001527532309 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 15, 15, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527532309 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 Building ZINC001527532309 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527532309 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 296) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1c(Cl)cccc1Cl) `ZINC001527532309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527532309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001527532309 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 3, 16, 16, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 297) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1c(Cl)cccc1Cl) `ZINC001527532309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527532309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001527532309 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 15, 15, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527532309 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527532309 Building ZINC001527533588 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527533588 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/298 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C2CCC2)cn1) `ZINC001527533588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527533588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527533588 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C2CCC2)cn1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 10, 10, 10, 6, 6, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 4, 6, 6, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/299 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C2CCC2)cn1) `ZINC001527533588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527533588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527533588 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C2CCC2)cn1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 12, 12, 12, 5, 5, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3, 3, 5, 5, 12, 12, 12, 12, 12, 12, 12, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527533588 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 Building ZINC001527533588 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527533588 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 298) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C2CCC2)cn1) `ZINC001527533588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527533588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527533588 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C2CCC2)cn1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 10, 10, 10, 6, 6, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 4, 6, 6, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 299) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C2CCC2)cn1) `ZINC001527533588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527533588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527533588 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C2CCC2)cn1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 12, 12, 12, 5, 5, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3, 3, 5, 5, 12, 12, 12, 12, 12, 12, 12, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527533588 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527533588 Building ZINC001527542090 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527542090 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/300 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccsc2)c2ccc(Br)cc2)cn1) `ZINC001527542090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527542090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001527542090 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccsc2)c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 3, 3, 5, 13, 25, 25, 25, 25, 5, 9, 9, 8, 9, 9, 9, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 13, 13, 25, 25, 25, 9, 9, 9, 9, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/301 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccsc2)c2ccc(Br)cc2)cn1) `ZINC001527542090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527542090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001527542090 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccsc2)c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 4, 4, 6, 14, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 14, 14, 26, 26, 26, 9, 9, 9, 9, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527542090 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 Building ZINC001527542090 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527542090 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 300) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccsc2)c2ccc(Br)cc2)cn1) `ZINC001527542090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527542090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001527542090 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccsc2)c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 3, 3, 5, 13, 25, 25, 25, 25, 5, 9, 9, 8, 9, 9, 9, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 13, 13, 25, 25, 25, 9, 9, 9, 9, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 301) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccsc2)c2ccc(Br)cc2)cn1) `ZINC001527542090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527542090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001527542090 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccsc2)c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 4, 4, 6, 14, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 14, 14, 26, 26, 26, 9, 9, 9, 9, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527542090 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527542090 Building ZINC001527612084 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527612084 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/302 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/302' -> `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](C)CCc1ccc(OC(C)C)cc1) `ZINC001527612084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527612084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527612084 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccc(OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 14, 15, 15, 15, 15, 15, 40, 45, 45, 15, 15, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 6, 6, 6, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 45, 45, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/303 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/303' -> `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](C)CCc1ccc(OC(C)C)cc1) `ZINC001527612084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527612084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527612084 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccc(OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 40, 43, 43, 16, 16, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 43, 43, 43, 43, 43, 43, 43, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527612084 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 Building ZINC001527612084 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527612084 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 302) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](C)CCc1ccc(OC(C)C)cc1) `ZINC001527612084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527612084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527612084 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccc(OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 14, 15, 15, 15, 15, 15, 40, 45, 45, 15, 15, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 6, 6, 6, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 45, 45, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 303) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](C)CCc1ccc(OC(C)C)cc1) `ZINC001527612084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527612084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527612084 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccc(OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 40, 43, 43, 16, 16, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 43, 43, 43, 43, 43, 43, 43, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527612084 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612084 Building ZINC001527612085 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527612085 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/304 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/304' -> `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](C)CCc1ccc(OC(C)C)cc1) `ZINC001527612085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527612085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527612085 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccc(OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 16, 17, 17, 17, 17, 17, 41, 44, 44, 17, 17, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 7, 7, 7, 17, 17, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 44, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 147 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/305 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/305' -> `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](C)CCc1ccc(OC(C)C)cc1) `ZINC001527612085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527612085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527612085 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccc(OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 13, 14, 14, 14, 14, 14, 39, 45, 45, 14, 14, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 45, 45, 45, 45, 45, 45, 45, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527612085 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 Building ZINC001527612085 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527612085 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 304) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](C)CCc1ccc(OC(C)C)cc1) `ZINC001527612085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527612085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527612085 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccc(OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 16, 17, 17, 17, 17, 17, 41, 44, 44, 17, 17, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 7, 7, 7, 17, 17, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 44, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 147 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 305) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](C)CCc1ccc(OC(C)C)cc1) `ZINC001527612085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527612085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527612085 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccc(OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 13, 14, 14, 14, 14, 14, 39, 45, 45, 14, 14, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 45, 45, 45, 45, 45, 45, 45, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527612085 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527612085 Building ZINC001527715566 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527715566 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/306 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F) `ZINC001527715566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527715566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001527715566 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 15, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 11, 11, 11, 11, 11, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/307 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F) `ZINC001527715566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527715566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001527715566 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 15, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 11, 11, 11, 11, 11, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527715566 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 Building ZINC001527715566 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527715566 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 306) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F) `ZINC001527715566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527715566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001527715566 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 15, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 11, 11, 11, 11, 11, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 307) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F) `ZINC001527715566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527715566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001527715566 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 15, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 11, 11, 11, 11, 11, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527715566 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527715566 Building ZINC001527753650 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527753650 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/308 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cc(C)ccc1C) `ZINC001527753650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527753650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527753650 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cc(C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 11, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 11, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 58 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/309 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cc(C)ccc1C) `ZINC001527753650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527753650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527753650 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cc(C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 5, 12, 12, 12, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 5, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 74 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527753650 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 Building ZINC001527753650 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527753650 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 308) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cc(C)ccc1C) `ZINC001527753650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527753650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527753650 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cc(C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 11, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 11, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 58 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 309) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cc(C)ccc1C) `ZINC001527753650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527753650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001527753650 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cc(C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 5, 12, 12, 12, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 5, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 74 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527753650 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527753650 Building ZINC001527754153 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527754153 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/310 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccccc4F)[nH]c3c2)cc1Cl) `ZINC001527754153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527754153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527754153 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccccc4F)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 28, 28, 18, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 18, 18, 28, 28, 25, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/311 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccccc4F)[nH]c3c2)cc1Cl) `ZINC001527754153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527754153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527754153 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccccc4F)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 28, 28, 18, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 18, 18, 28, 28, 21, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527754153 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 Building ZINC001527754153 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527754153 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 310) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccccc4F)[nH]c3c2)cc1Cl) `ZINC001527754153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527754153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527754153 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccccc4F)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 28, 28, 18, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 18, 18, 28, 28, 25, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 311) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccccc4F)[nH]c3c2)cc1Cl) `ZINC001527754153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527754153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527754153 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccccc4F)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 28, 28, 18, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 18, 18, 28, 28, 21, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527754153 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527754153 Building ZINC001527786040 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527786040 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/312 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2ccc(C)c(C)c2)CC1) `ZINC001527786040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527786040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527786040 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2ccc(C)c(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 14, 28, 28, 28, 28, 28, 28, 28, 4, 4, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/313 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2ccc(C)c(C)c2)CC1) `ZINC001527786040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527786040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527786040 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2ccc(C)c(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 18, 37, 37, 35, 37, 37, 37, 37, 5, 5, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 5, 5, 5, 5, 5, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527786040 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 Building ZINC001527786040 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527786040 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 312) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2ccc(C)c(C)c2)CC1) `ZINC001527786040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527786040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527786040 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2ccc(C)c(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 14, 28, 28, 28, 28, 28, 28, 28, 4, 4, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 313) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2ccc(C)c(C)c2)CC1) `ZINC001527786040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527786040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001527786040 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2ccc(C)c(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 18, 37, 37, 35, 37, 37, 37, 37, 5, 5, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 5, 5, 5, 5, 5, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527786040 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527786040 Building ZINC001527797330 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527797330 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/314 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2C(F)(F)F)cc1Cl) `ZINC001527797330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527797330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527797330 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 21, 28, 28, 7, 7, 7, 7, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/315 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2C(F)(F)F)cc1Cl) `ZINC001527797330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527797330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527797330 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 22, 28, 28, 7, 7, 7, 7, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527797330 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 Building ZINC001527797330 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527797330 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 314) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2C(F)(F)F)cc1Cl) `ZINC001527797330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527797330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527797330 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 21, 28, 28, 7, 7, 7, 7, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 315) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2C(F)(F)F)cc1Cl) `ZINC001527797330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527797330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527797330 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 22, 28, 28, 7, 7, 7, 7, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527797330 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527797330 Building ZINC001527961585 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527961585 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/316 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2cccc(F)c2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527961585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527961585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527961585 none O=C(NCc1ccc(OCc2cccc(F)c2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 13, 13, 9, 13, 22, 22, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 22, 22, 50, 50, 50, 50, 13, 13, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/317 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2cccc(F)c2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527961585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527961585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527961585 none O=C(NCc1ccc(OCc2cccc(F)c2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 13, 13, 8, 8, 22, 22, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 22, 22, 50, 50, 50, 50, 13, 13, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527961585 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 Building ZINC001527961585 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527961585 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 316) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2cccc(F)c2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527961585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527961585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527961585 none O=C(NCc1ccc(OCc2cccc(F)c2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 13, 13, 9, 13, 22, 22, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 22, 22, 50, 50, 50, 50, 13, 13, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 317) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2cccc(F)c2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001527961585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527961585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001527961585 none O=C(NCc1ccc(OCc2cccc(F)c2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 13, 13, 8, 8, 22, 22, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 22, 22, 50, 50, 50, 50, 13, 13, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527961585 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527961585 Building ZINC001527985978 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527985978 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/318 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(Br)c1) `ZINC001527985978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527985978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527985978 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 20, 24, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 24, 24, 24, 24, 24, 7, 7, 7, 7, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [43, 17, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/319 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(Br)c1) `ZINC001527985978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527985978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527985978 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 8, 22, 26, 8, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 21, 21, 12, 21, 21, 21, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 8, 8, 8, 8, 2, 2, 2, 2, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527985978 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 Building ZINC001527985978 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001527985978 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 318) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(Br)c1) `ZINC001527985978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001527985978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527985978 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 20, 24, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 24, 24, 24, 24, 24, 7, 7, 7, 7, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [43, 17, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 319) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(Br)c1) `ZINC001527985978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001527985978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001527985978 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 8, 22, 26, 8, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 21, 21, 12, 21, 21, 21, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 8, 8, 8, 8, 2, 2, 2, 2, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001527985978 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001527985978 Building ZINC001528003373 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528003373 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/320 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCCOc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001528003373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528003373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001528003373 none O=C(NCc1ccc(OCCOc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 7, 4, 7, 18, 18, 18, 32, 33, 33, 32, 32, 33, 33, 7, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 7, 7, 18, 18, 18, 18, 33, 33, 33, 33, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/321 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCCOc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001528003373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528003373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001528003373 none O=C(NCc1ccc(OCCOc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 6, 6, 5, 6, 17, 17, 17, 32, 33, 33, 32, 32, 33, 33, 6, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 17, 17, 17, 17, 33, 33, 33, 33, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528003373 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 Building ZINC001528003373 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528003373 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 320) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCCOc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001528003373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528003373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001528003373 none O=C(NCc1ccc(OCCOc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 7, 4, 7, 18, 18, 18, 32, 33, 33, 32, 32, 33, 33, 7, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 7, 7, 18, 18, 18, 18, 33, 33, 33, 33, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 321) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCCOc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001528003373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528003373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001528003373 none O=C(NCc1ccc(OCCOc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 6, 6, 5, 6, 17, 17, 17, 32, 33, 33, 32, 32, 33, 33, 6, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 17, 17, 17, 17, 33, 33, 33, 33, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528003373 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528003373 Building ZINC001528017622 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528017622 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/322 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Cl) `ZINC001528017622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528017622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001528017622 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 7, 7, 7, 30, 30, 30, 16, 30, 30, 30, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 7, 30, 17, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/323 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Cl) `ZINC001528017622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528017622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001528017622 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 15, 15, 7, 15, 15, 4, 4, 4, 7, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528017622 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 Building ZINC001528017622 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528017622 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 322) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Cl) `ZINC001528017622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528017622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001528017622 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 7, 7, 7, 30, 30, 30, 16, 30, 30, 30, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 7, 30, 17, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 323) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Cl) `ZINC001528017622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528017622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001528017622 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 15, 15, 7, 15, 15, 4, 4, 4, 7, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528017622 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528017622 Building ZINC001528027278 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528027278 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/324 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccc(Cl)cc2C1) `ZINC001528027278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528027278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528027278 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccc(Cl)cc2C1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/325 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccc(Cl)cc2C1) `ZINC001528027278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528027278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528027278 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccc(Cl)cc2C1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528027278 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 Building ZINC001528027278 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528027278 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 324) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccc(Cl)cc2C1) `ZINC001528027278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528027278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528027278 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccc(Cl)cc2C1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 325) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccc(Cl)cc2C1) `ZINC001528027278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528027278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528027278 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccc(Cl)cc2C1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528027278 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528027278 Building ZINC001528032219 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528032219 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/326 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1C(=O)c1ccc[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528032219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528032219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528032219 none O=C(Nc1ccc(Cl)cc1C(=O)c1ccc[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 18, 18, 30, 30, 30, 30, 30, 1, 1, 1, 10, 10, 10, 10, 10, 5, 12, 12, 12, 30, 30, 30, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/327 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1C(=O)c1ccc[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528032219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528032219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528032219 none O=C(Nc1ccc(Cl)cc1C(=O)c1ccc[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 18, 18, 31, 31, 31, 31, 31, 1, 1, 1, 10, 10, 10, 10, 10, 5, 12, 12, 12, 31, 31, 31, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528032219 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 Building ZINC001528032219 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528032219 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 326) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1C(=O)c1ccc[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528032219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528032219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528032219 none O=C(Nc1ccc(Cl)cc1C(=O)c1ccc[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 18, 18, 30, 30, 30, 30, 30, 1, 1, 1, 10, 10, 10, 10, 10, 5, 12, 12, 12, 30, 30, 30, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 327) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1C(=O)c1ccc[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528032219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528032219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528032219 none O=C(Nc1ccc(Cl)cc1C(=O)c1ccc[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 18, 18, 31, 31, 31, 31, 31, 1, 1, 1, 10, 10, 10, 10, 10, 5, 12, 12, 12, 31, 31, 31, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528032219 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528032219 Building ZINC001528045712 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528045712 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/328 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001528045712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528045712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001528045712 none O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 6, 28, 28, 29, 29, 29, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 111 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/329 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001528045712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528045712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001528045712 none O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 28, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 6, 28, 28, 30, 30, 30, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 113 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528045712 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 Building ZINC001528045712 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528045712 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 328) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001528045712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528045712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001528045712 none O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 6, 28, 28, 29, 29, 29, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 111 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 329) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001528045712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528045712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001528045712 none O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 28, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 6, 28, 28, 30, 30, 30, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 113 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528045712 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528045712 Building ZINC001528055658 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528055658 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/330 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001528055658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528055658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001528055658 none CCOc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.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, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 29, 29, 29, 29, 29, 6, 6, 6, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/331 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001528055658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528055658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001528055658 none CCOc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.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, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 34, 34, 34, 34, 34, 9, 9, 9, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528055658 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 Building ZINC001528055658 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528055658 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 330) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001528055658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528055658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001528055658 none CCOc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.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, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 29, 29, 29, 29, 29, 6, 6, 6, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 331) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001528055658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528055658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001528055658 none CCOc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.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, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 34, 34, 34, 34, 34, 9, 9, 9, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528055658 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528055658 Building ZINC001528078070 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528078070 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/332 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001528078070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528078070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078070 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 8, 3, 14, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 26, 26, 25, 25, 25, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 25, 25, 26, 26, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/333 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001528078070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528078070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078070 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 5, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 26, 26, 26, 26, 26] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528078070 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 Building ZINC001528078070 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528078070 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 332) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001528078070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528078070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078070 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 8, 3, 14, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 26, 26, 25, 25, 25, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 25, 25, 26, 26, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 333) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001528078070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528078070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078070 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 5, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 26, 26, 26, 26, 26] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528078070 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078070 Building ZINC001528078071 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528078071 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/334 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001528078071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528078071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078071 none C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 9, 5, 20, 20, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 27, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/335 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001528078071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528078071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078071 none C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 26, 15, 21, 21, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 29, 29, 29, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528078071 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 Building ZINC001528078071 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528078071 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 334) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001528078071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528078071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078071 none C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 9, 5, 20, 20, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 27, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 335) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001528078071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528078071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078071 none C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 26, 15, 21, 21, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 29, 29, 29, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528078071 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078071 Building ZINC001528078072 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528078072 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/336 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@@H](C)O1) `ZINC001528078072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528078072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078072 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 26, 14, 19, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 27, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/337 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@@H](C)O1) `ZINC001528078072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528078072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078072 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 13, 4, 18, 18, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 18, 18, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 27, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528078072 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 Building ZINC001528078072 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528078072 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 336) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@@H](C)O1) `ZINC001528078072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528078072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078072 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 26, 14, 19, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 27, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 337) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@@H](C)O1) `ZINC001528078072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528078072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528078072 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C(F)(F)F)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 15, 15, 15, 5, 5, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 13, 4, 18, 18, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 18, 18, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 27, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528078072 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528078072 Building ZINC001528090131 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528090131 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/338 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(Cl)cc2)CCCC1) `ZINC001528090131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528090131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528090131 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(Cl)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 21, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/339 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(Cl)cc2)CCCC1) `ZINC001528090131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528090131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528090131 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(Cl)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 11, 11, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528090131 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 Building ZINC001528090131 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528090131 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 338) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(Cl)cc2)CCCC1) `ZINC001528090131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528090131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528090131 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(Cl)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 21, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 339) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(Cl)cc2)CCCC1) `ZINC001528090131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528090131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001528090131 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(Cl)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 11, 11, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528090131 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528090131 Building ZINC001528132816 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528132816 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/340 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(CC(=O)Nc1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528132816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528132816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001528132816 none CC(C)(C)N(CC(=O)Nc1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 5, 6, 12, 28, 28, 28, 45, 45, 37, 40, 45, 45, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 28, 45, 45, 45, 45, 4, 2, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/341 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(CC(=O)Nc1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528132816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528132816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001528132816 none CC(C)(C)N(CC(=O)Nc1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 5, 6, 10, 30, 30, 30, 46, 46, 42, 46, 46, 46, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 30, 46, 46, 46, 46, 4, 1, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 175 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528132816 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 Building ZINC001528132816 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528132816 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 340) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(CC(=O)Nc1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528132816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528132816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001528132816 none CC(C)(C)N(CC(=O)Nc1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 5, 6, 12, 28, 28, 28, 45, 45, 37, 40, 45, 45, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 28, 45, 45, 45, 45, 4, 2, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 341) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(CC(=O)Nc1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528132816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528132816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001528132816 none CC(C)(C)N(CC(=O)Nc1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 5, 6, 10, 30, 30, 30, 46, 46, 42, 46, 46, 46, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 30, 46, 46, 46, 46, 4, 1, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 175 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528132816 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528132816 Building ZINC001528134227 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528134227 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/342 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC(c1ccc(F)cc1)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528134227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528134227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528134227 none O=C(NC(c1ccc(F)cc1)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 17, 17, 17, 17, 17, 17, 8, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 4, 8, 17, 17, 17, 17, 16, 16, 16, 16, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/343 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC(c1ccc(F)cc1)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528134227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528134227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528134227 none O=C(NC(c1ccc(F)cc1)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 17, 17, 8, 17, 17, 17, 8, 16, 16, 8, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 4, 8, 17, 17, 17, 17, 16, 16, 16, 16, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528134227 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 Building ZINC001528134227 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528134227 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 342) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c1ccc(F)cc1)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528134227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528134227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528134227 none O=C(NC(c1ccc(F)cc1)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 17, 17, 17, 17, 17, 17, 8, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 4, 8, 17, 17, 17, 17, 16, 16, 16, 16, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 343) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c1ccc(F)cc1)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528134227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528134227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528134227 none O=C(NC(c1ccc(F)cc1)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 17, 17, 8, 17, 17, 17, 8, 16, 16, 8, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 4, 8, 17, 17, 17, 17, 16, 16, 16, 16, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528134227 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528134227 Building ZINC001528144837 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528144837 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/344 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCc2cccc(F)c2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001528144837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528144837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001528144837 none Cc1cc(OCc2cccc(F)c2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 6, 6, 34, 34, 34, 34, 34, 34, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 6, 6, 34, 34, 34, 34, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 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: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/345 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCc2cccc(F)c2)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001528144837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528144837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001528144837 none Cc1cc(OCc2cccc(F)c2)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 36, 36, 36, 36, 36, 36, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 6, 6, 36, 36, 36, 36, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 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: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528144837 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 Building ZINC001528144837 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528144837 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 344) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OCc2cccc(F)c2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001528144837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528144837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001528144837 none Cc1cc(OCc2cccc(F)c2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 6, 6, 34, 34, 34, 34, 34, 34, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 6, 6, 34, 34, 34, 34, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 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: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 345) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OCc2cccc(F)c2)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001528144837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528144837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001528144837 none Cc1cc(OCc2cccc(F)c2)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 36, 36, 36, 36, 36, 36, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 6, 6, 36, 36, 36, 36, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 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: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528144837 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528144837 Building ZINC001528175160 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528175160 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/346 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528175160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528175160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528175160 none O=C(N1CC[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 16, 16, 16, 16, 16, 29, 29, 16, 18, 29, 29, 29, 29, 29, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 29, 29, 29, 29, 16, 16, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/347 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528175160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528175160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528175160 none O=C(N1CC[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 18, 18, 18, 18, 18, 32, 32, 25, 25, 32, 32, 32, 32, 32, 18, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 32, 32, 32, 32, 18, 18, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528175160 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 Building ZINC001528175160 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528175160 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 346) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528175160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528175160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528175160 none O=C(N1CC[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 16, 16, 16, 16, 16, 29, 29, 16, 18, 29, 29, 29, 29, 29, 16, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 16, 29, 29, 29, 29, 16, 16, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 347) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528175160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528175160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528175160 none O=C(N1CC[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 18, 18, 18, 18, 18, 32, 32, 25, 25, 32, 32, 32, 32, 32, 18, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 32, 32, 32, 32, 18, 18, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528175160 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175160 Building ZINC001528175161 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528175161 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/348 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528175161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528175161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528175161 none O=C(N1CC[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 19, 19, 19, 19, 19, 31, 31, 19, 19, 31, 31, 31, 31, 31, 19, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 19, 19, 31, 31, 31, 31, 19, 19, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/349 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528175161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528175161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528175161 none O=C(N1CC[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 17, 17, 17, 17, 17, 29, 29, 17, 17, 29, 29, 29, 29, 29, 17, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 29, 29, 29, 29, 17, 17, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528175161 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 Building ZINC001528175161 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528175161 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 348) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528175161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528175161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528175161 none O=C(N1CC[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 19, 19, 19, 19, 19, 31, 31, 19, 19, 31, 31, 31, 31, 31, 19, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 19, 19, 31, 31, 31, 31, 19, 19, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 349) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528175161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528175161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001528175161 none O=C(N1CC[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 17, 17, 17, 17, 17, 29, 29, 17, 17, 29, 29, 29, 29, 29, 17, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 29, 29, 29, 29, 17, 17, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528175161 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528175161 Building ZINC001528229675 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528229675 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/350 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1c1nc(c2ccccc2)no1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528229675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528229675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001528229675 none O=C(N1CCCC[C@H]1c1nc(c2ccccc2)no1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 44, 44, 44, 45, 45, 44, 45, 45, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 45, 45, 44, 45, 45, 3, 1, 3] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/351 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1c1nc(c2ccccc2)no1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528229675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528229675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001528229675 none O=C(N1CCCC[C@H]1c1nc(c2ccccc2)no1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 43, 43, 43, 47, 47, 45, 47, 47, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 47, 47, 45, 47, 47, 3, 1, 3] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528229675 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 Building ZINC001528229675 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528229675 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 350) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1c1nc(c2ccccc2)no1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528229675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528229675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001528229675 none O=C(N1CCCC[C@H]1c1nc(c2ccccc2)no1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 44, 44, 44, 45, 45, 44, 45, 45, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 45, 45, 44, 45, 45, 3, 1, 3] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 351) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1c1nc(c2ccccc2)no1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528229675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528229675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001528229675 none O=C(N1CCCC[C@H]1c1nc(c2ccccc2)no1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 43, 43, 43, 47, 47, 45, 47, 47, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 47, 47, 45, 47, 47, 3, 1, 3] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528229675 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229675 Building ZINC001528229676 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528229676 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/352 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1c1nc(c2ccccc2)no1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528229676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528229676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001528229676 none O=C(N1CCCC[C@@H]1c1nc(c2ccccc2)no1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 43, 43, 43, 46, 46, 45, 46, 46, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 46, 46, 46, 46, 46, 3, 1, 3] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/353 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1c1nc(c2ccccc2)no1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528229676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528229676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001528229676 none O=C(N1CCCC[C@@H]1c1nc(c2ccccc2)no1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 44, 44, 44, 46, 46, 44, 46, 46, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 46, 46, 46, 46, 46, 3, 1, 3] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528229676 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 Building ZINC001528229676 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528229676 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 352) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1c1nc(c2ccccc2)no1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528229676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528229676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001528229676 none O=C(N1CCCC[C@@H]1c1nc(c2ccccc2)no1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 43, 43, 43, 46, 46, 45, 46, 46, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 46, 46, 46, 46, 46, 3, 1, 3] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 353) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1c1nc(c2ccccc2)no1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528229676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528229676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001528229676 none O=C(N1CCCC[C@@H]1c1nc(c2ccccc2)no1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 44, 44, 44, 46, 46, 44, 46, 46, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 46, 46, 46, 46, 46, 3, 1, 3] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528229676 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528229676 Building ZINC001528263233 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001528263233 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/354 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [16, 8, 16, 26, 35, 35, 28, 35, 35, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 26, 26, 35, 35, 35, 35, 35, 8, 8, 8, 8, 4, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/355 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [16, 8, 16, 26, 35, 35, 28, 35, 35, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 26, 26, 35, 35, 35, 35, 35, 8, 8, 8, 8, 4, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/356 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/356' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [18, 11, 18, 26, 35, 35, 28, 35, 35, 11, 11, 9, 11, 11, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 26, 26, 35, 35, 35, 35, 35, 11, 11, 11, 11, 5, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/357 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/357' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [18, 11, 18, 26, 35, 35, 28, 35, 35, 11, 11, 9, 11, 11, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 26, 26, 35, 35, 35, 35, 35, 11, 11, 11, 11, 5, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528263233 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 Building ZINC001528263233 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001528263233 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 354) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [16, 8, 16, 26, 35, 35, 28, 35, 35, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 26, 26, 35, 35, 35, 35, 35, 8, 8, 8, 8, 4, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 355) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [16, 8, 16, 26, 35, 35, 28, 35, 35, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 26, 26, 35, 35, 35, 35, 35, 8, 8, 8, 8, 4, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 356) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [18, 11, 18, 26, 35, 35, 28, 35, 35, 11, 11, 9, 11, 11, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 26, 26, 35, 35, 35, 35, 35, 11, 11, 11, 11, 5, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 357) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [18, 11, 18, 26, 35, 35, 28, 35, 35, 11, 11, 9, 11, 11, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 26, 26, 35, 35, 35, 35, 35, 11, 11, 11, 11, 5, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528263233 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 Building ZINC001528263233 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001528263233 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 354) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [16, 8, 16, 26, 35, 35, 28, 35, 35, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 26, 26, 35, 35, 35, 35, 35, 8, 8, 8, 8, 4, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 355) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [16, 8, 16, 26, 35, 35, 28, 35, 35, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 26, 26, 35, 35, 35, 35, 35, 8, 8, 8, 8, 4, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 356) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [18, 11, 18, 26, 35, 35, 28, 35, 35, 11, 11, 9, 11, 11, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 26, 26, 35, 35, 35, 35, 35, 11, 11, 11, 11, 5, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 357) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [18, 11, 18, 26, 35, 35, 28, 35, 35, 11, 11, 9, 11, 11, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 26, 26, 35, 35, 35, 35, 35, 11, 11, 11, 11, 5, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528263233 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 Building ZINC001528263233 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001528263233 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 354) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [16, 8, 16, 26, 35, 35, 28, 35, 35, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 26, 26, 35, 35, 35, 35, 35, 8, 8, 8, 8, 4, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 355) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [16, 8, 16, 26, 35, 35, 28, 35, 35, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 26, 26, 35, 35, 35, 35, 35, 8, 8, 8, 8, 4, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 356) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [18, 11, 18, 26, 35, 35, 28, 35, 35, 11, 11, 9, 11, 11, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 26, 26, 35, 35, 35, 35, 35, 11, 11, 11, 11, 5, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 357) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528263233.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001528263233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001528263233 none CN(Cc1ccccc1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [18, 11, 18, 26, 35, 35, 28, 35, 35, 11, 11, 9, 11, 11, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 26, 26, 35, 35, 35, 35, 35, 11, 11, 11, 11, 5, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528263233 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528263233 Building ZINC001528275600 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528275600 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/358 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)nc2cc(Cl)c(Cl)cc21) `ZINC001528275600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528275600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001528275600 none Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)nc2cc(Cl)c(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 11, 1, 11, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 23, 23] 32 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/359 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)nc2cc(Cl)c(Cl)cc21) `ZINC001528275600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528275600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001528275600 none Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)nc2cc(Cl)c(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 11, 1, 11, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 23, 23] 32 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528275600 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 Building ZINC001528275600 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528275600 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 358) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)nc2cc(Cl)c(Cl)cc21) `ZINC001528275600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528275600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001528275600 none Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)nc2cc(Cl)c(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 11, 1, 11, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 23, 23] 32 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 359) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)nc2cc(Cl)c(Cl)cc21) `ZINC001528275600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528275600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001528275600 none Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)nc2cc(Cl)c(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 11, 1, 11, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 23, 23] 32 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528275600 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528275600 Building ZINC001528280374 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528280374 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/360 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001528280374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528280374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001528280374 none CCN(CC)CCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 4, 15, 16, 4, 1, 1, 1, 2, 3, 3, 2, 2, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 2, 2, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [6, 7, 8, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/361 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001528280374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528280374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001528280374 none CCN(CC)CCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 14, 15, 4, 1, 1, 1, 2, 3, 3, 2, 2, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 2, 2, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [6, 7, 8, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528280374 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 Building ZINC001528280374 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528280374 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 360) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001528280374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528280374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001528280374 none CCN(CC)CCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 4, 15, 16, 4, 1, 1, 1, 2, 3, 3, 2, 2, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 2, 2, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [6, 7, 8, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 361) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001528280374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528280374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001528280374 none CCN(CC)CCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 14, 15, 4, 1, 1, 1, 2, 3, 3, 2, 2, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 2, 2, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [6, 7, 8, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528280374 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528280374 Building ZINC001528296493 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528296493 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/362 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1) `ZINC001528296493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528296493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001528296493 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 8, 17, 20, 31, 34, 34, 8, 20, 23, 23, 22, 23, 23, 20, 22, 22, 20, 22, 22, 2, 2, 2, 2, 2, 2, 17, 17, 20, 20, 31, 31, 34, 34, 34, 34, 34, 34, 20, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 224 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/363 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1) `ZINC001528296493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528296493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001528296493 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 6, 15, 18, 30, 32, 32, 6, 18, 20, 20, 19, 20, 20, 18, 21, 21, 18, 21, 21, 1, 1, 1, 1, 1, 1, 15, 15, 18, 18, 30, 30, 32, 32, 32, 32, 32, 32, 18, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 220 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528296493 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 Building ZINC001528296493 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528296493 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 362) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1) `ZINC001528296493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528296493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001528296493 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 8, 17, 20, 31, 34, 34, 8, 20, 23, 23, 22, 23, 23, 20, 22, 22, 20, 22, 22, 2, 2, 2, 2, 2, 2, 17, 17, 20, 20, 31, 31, 34, 34, 34, 34, 34, 34, 20, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 224 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 363) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1) `ZINC001528296493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528296493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001528296493 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)C(c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 6, 15, 18, 30, 32, 32, 6, 18, 20, 20, 19, 20, 20, 18, 21, 21, 18, 21, 21, 1, 1, 1, 1, 1, 1, 15, 15, 18, 18, 30, 30, 32, 32, 32, 32, 32, 32, 18, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 220 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528296493 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528296493 Building ZINC001528403838 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528403838 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/364 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccccc2Cl)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528403838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528403838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528403838 none O=C(NCC1(c2ccccc2Cl)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/365 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccccc2Cl)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528403838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528403838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528403838 none O=C(NCC1(c2ccccc2Cl)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 15, 15, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528403838 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 Building ZINC001528403838 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528403838 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 364) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccccc2Cl)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528403838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528403838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528403838 none O=C(NCC1(c2ccccc2Cl)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 365) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccccc2Cl)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001528403838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528403838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528403838 none O=C(NCC1(c2ccccc2Cl)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 15, 15, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528403838 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528403838 Building ZINC001528409315 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528409315 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/366 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)c(C)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001528409315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528409315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528409315 none COc1cc(C)c(C)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 5, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 2, 3, 3, 3, 15, 15, 5, 15, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/367 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)c(C)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001528409315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528409315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528409315 none COc1cc(C)c(C)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 5, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528409315 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 Building ZINC001528409315 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528409315 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 366) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c(C)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001528409315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528409315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528409315 none COc1cc(C)c(C)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 5, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 2, 3, 3, 3, 15, 15, 5, 15, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 367) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c(C)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001528409315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528409315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528409315 none COc1cc(C)c(C)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 5, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528409315 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409315 Building ZINC001528409335 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528409335 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/368 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1) `ZINC001528409335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528409335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001528409335 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 16, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 4, 4, 2, 2, 2, 2, 2, 2, 3, 4, 4, 16, 19, 19, 19, 19, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/369 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1) `ZINC001528409335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528409335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001528409335 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 16, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 4, 4, 2, 2, 2, 2, 2, 2, 3, 4, 4, 16, 19, 19, 19, 19, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528409335 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 Building ZINC001528409335 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528409335 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 368) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1) `ZINC001528409335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528409335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001528409335 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 16, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 4, 4, 2, 2, 2, 2, 2, 2, 3, 4, 4, 16, 19, 19, 19, 19, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 369) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1) `ZINC001528409335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528409335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001528409335 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 16, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 4, 4, 2, 2, 2, 2, 2, 2, 3, 4, 4, 16, 19, 19, 19, 19, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528409335 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528409335 Building ZINC001528445718 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528445718 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/370 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)c(Cl)c1Cl)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001528445718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528445718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528445718 none O=C(Nc1ccc(Br)c(Cl)c1Cl)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 16, 1, 16, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 17, 9, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 20, 20, 11, 4, 17, 17, 11, 20, 20, 11, 20, 20, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/371 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)c(Cl)c1Cl)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001528445718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528445718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528445718 none O=C(Nc1ccc(Br)c(Cl)c1Cl)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 16, 1, 16, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 17, 9, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 20, 20, 11, 4, 17, 17, 11, 20, 20, 20, 20, 20, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528445718 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 Building ZINC001528445718 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528445718 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 370) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)c(Cl)c1Cl)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001528445718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528445718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528445718 none O=C(Nc1ccc(Br)c(Cl)c1Cl)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 16, 1, 16, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 17, 9, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 20, 20, 11, 4, 17, 17, 11, 20, 20, 11, 20, 20, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 371) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)c(Cl)c1Cl)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001528445718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528445718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528445718 none O=C(Nc1ccc(Br)c(Cl)c1Cl)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 16, 1, 16, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 17, 9, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 20, 20, 11, 4, 17, 17, 11, 20, 20, 20, 20, 20, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528445718 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528445718 Building ZINC001528459172 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528459172 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/372 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br) `ZINC001528459172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528459172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001528459172 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 21, 21, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 6, 6, 4, 8, 8, 4, 8, 8, 21, 21, 21, 25, 25, 25, 21, 21, 2, 6, 6, 2, 6, 6, 6, 6, 8, 8, 4, 8, 8, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/373 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br) `ZINC001528459172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528459172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001528459172 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 12, 17, 17, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 10, 10, 6, 10, 10, 17, 17, 17, 25, 25, 25, 17, 17, 3, 6, 6, 2, 6, 6, 6, 6, 10, 10, 6, 10, 10, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528459172 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 Building ZINC001528459172 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528459172 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 372) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br) `ZINC001528459172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528459172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001528459172 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 21, 21, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 6, 6, 4, 8, 8, 4, 8, 8, 21, 21, 21, 25, 25, 25, 21, 21, 2, 6, 6, 2, 6, 6, 6, 6, 8, 8, 4, 8, 8, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 373) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br) `ZINC001528459172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528459172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001528459172 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 12, 17, 17, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 10, 10, 6, 10, 10, 17, 17, 17, 25, 25, 25, 17, 17, 3, 6, 6, 2, 6, 6, 6, 6, 10, 10, 6, 10, 10, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528459172 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459172 Building ZINC001528459173 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528459173 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/374 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br) `ZINC001528459173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528459173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001528459173 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 17, 17, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 10, 10, 6, 10, 10, 17, 17, 17, 26, 26, 26, 17, 17, 3, 6, 6, 2, 6, 6, 6, 6, 10, 10, 6, 10, 10, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/375 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br) `ZINC001528459173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528459173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001528459173 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 21, 21, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 6, 6, 4, 8, 8, 4, 8, 8, 21, 21, 21, 25, 25, 25, 21, 21, 2, 6, 6, 2, 6, 6, 6, 6, 8, 8, 4, 8, 8, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528459173 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 Building ZINC001528459173 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528459173 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 374) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br) `ZINC001528459173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528459173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001528459173 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 17, 17, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 10, 10, 6, 10, 10, 17, 17, 17, 26, 26, 26, 17, 17, 3, 6, 6, 2, 6, 6, 6, 6, 10, 10, 6, 10, 10, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 375) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br) `ZINC001528459173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528459173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001528459173 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2ccccc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 21, 21, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 6, 6, 4, 8, 8, 4, 8, 8, 21, 21, 21, 25, 25, 25, 21, 21, 2, 6, 6, 2, 6, 6, 6, 6, 8, 8, 4, 8, 8, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528459173 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528459173 Building ZINC001528460398 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528460398 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/376 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)c(C(F)(F)F)c2)n1) `ZINC001528460398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528460398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001528460398 none Cc1cc(C)n(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)c(C(F)(F)F)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 4, 5, 5, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/377 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)c(C(F)(F)F)c2)n1) `ZINC001528460398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528460398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001528460398 none Cc1cc(C)n(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)c(C(F)(F)F)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 4, 5, 5, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528460398 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 Building ZINC001528460398 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528460398 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 376) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)c(C(F)(F)F)c2)n1) `ZINC001528460398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528460398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001528460398 none Cc1cc(C)n(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)c(C(F)(F)F)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 4, 5, 5, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 377) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)c(C(F)(F)F)c2)n1) `ZINC001528460398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528460398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001528460398 none Cc1cc(C)n(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)c(C(F)(F)F)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 4, 5, 5, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528460398 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528460398 Building ZINC001528490186 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528490186 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/378 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)c2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)nc21) `ZINC001528490186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528490186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001528490186 none COc1ccc(Br)c2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [37, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 19, 37, 37, 37, 19, 19, 11, 6, 6, 6, 6] 48 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/379 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)c2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)nc21) `ZINC001528490186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528490186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001528490186 none COc1ccc(Br)c2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [37, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 19, 37, 37, 37, 19, 19, 11, 6, 6, 6, 6] 48 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528490186 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 Building ZINC001528490186 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528490186 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 378) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)c2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)nc21) `ZINC001528490186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528490186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001528490186 none COc1ccc(Br)c2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [37, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 19, 37, 37, 37, 19, 19, 11, 6, 6, 6, 6] 48 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 379) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)c2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)nc21) `ZINC001528490186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528490186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001528490186 none COc1ccc(Br)c2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [37, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 19, 37, 37, 37, 19, 19, 11, 6, 6, 6, 6] 48 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528490186 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528490186 Building ZINC001528492783 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528492783 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/380 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cccc2c1N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)CC2) `ZINC001528492783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528492783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528492783 none CCc1cccc2c1N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 4, 28, 28, 28, 28, 28, 28, 4, 4, 5, 5, 9, 9, 9, 9, 9, 5, 5, 5, 4, 4, 4, 28, 28, 4, 28, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 95 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/381 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cccc2c1N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)CC2) `ZINC001528492783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528492783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528492783 none CCc1cccc2c1N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 4, 4, 4, 22, 22, 5, 22, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 76 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528492783 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 Building ZINC001528492783 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528492783 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 380) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cccc2c1N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)CC2) `ZINC001528492783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528492783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528492783 none CCc1cccc2c1N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 4, 28, 28, 28, 28, 28, 28, 4, 4, 5, 5, 9, 9, 9, 9, 9, 5, 5, 5, 4, 4, 4, 28, 28, 4, 28, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 95 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 381) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cccc2c1N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)CC2) `ZINC001528492783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528492783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528492783 none CCc1cccc2c1N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 4, 4, 4, 22, 22, 5, 22, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 76 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528492783 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528492783 Building ZINC001528507748 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528507748 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/382 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001528507748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528507748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001528507748 none O=C(Nc1ccccc1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 21, 34, 34, 21, 34, 34, 9, 13, 13, 3, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 21, 34, 34, 21, 34, 34, 13, 13, 3, 10, 10, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/383 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001528507748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528507748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001528507748 none O=C(Nc1ccccc1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 22, 34, 34, 33, 34, 34, 9, 14, 14, 3, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 22, 34, 34, 34, 34, 34, 14, 14, 3, 10, 10, 14, 14] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528507748 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 Building ZINC001528507748 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528507748 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 382) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001528507748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528507748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001528507748 none O=C(Nc1ccccc1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 21, 34, 34, 21, 34, 34, 9, 13, 13, 3, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 21, 34, 34, 21, 34, 34, 13, 13, 3, 10, 10, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 383) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001528507748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528507748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001528507748 none O=C(Nc1ccccc1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 22, 34, 34, 33, 34, 34, 9, 14, 14, 3, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 22, 34, 34, 34, 34, 34, 14, 14, 3, 10, 10, 14, 14] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528507748 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528507748 Building ZINC001528543865 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528543865 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/384 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC001528543865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528543865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001528543865 none CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 8, 15, 16, 8, 3, 2, 3, 7, 14, 14, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 7, 7, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 101 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/385 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC001528543865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528543865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001528543865 none CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 9, 17, 18, 9, 3, 2, 3, 6, 13, 13, 13, 13, 13, 13, 13, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 6, 6, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528543865 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 Building ZINC001528543865 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528543865 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 384) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC001528543865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528543865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001528543865 none CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 8, 15, 16, 8, 3, 2, 3, 7, 14, 14, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 7, 7, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 101 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 385) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC001528543865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528543865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001528543865 none CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 9, 17, 18, 9, 3, 2, 3, 6, 13, 13, 13, 13, 13, 13, 13, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 6, 6, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528543865 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543865 Building ZINC001528543884 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528543884 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/386 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCN1CCCC1)Cc1ccc(Cl)c(Cl)c1) `ZINC001528543884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528543884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001528543884 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCN1CCCC1)Cc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 3, 7, 11, 22, 22, 22, 22, 3, 5, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 34, 4, 5, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/387 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCN1CCCC1)Cc1ccc(Cl)c(Cl)c1) `ZINC001528543884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528543884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001528543884 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCN1CCCC1)Cc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 8, 12, 22, 22, 22, 22, 4, 7, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 8, 8, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 7, 7, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528543884 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 Building ZINC001528543884 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528543884 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 386) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCN1CCCC1)Cc1ccc(Cl)c(Cl)c1) `ZINC001528543884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528543884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001528543884 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCN1CCCC1)Cc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 3, 7, 11, 22, 22, 22, 22, 3, 5, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 34, 4, 5, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 387) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCN1CCCC1)Cc1ccc(Cl)c(Cl)c1) `ZINC001528543884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528543884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001528543884 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCN1CCCC1)Cc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 8, 12, 22, 22, 22, 22, 4, 7, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 8, 8, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 7, 7, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528543884 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528543884 Building ZINC001528669757 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528669757 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/388 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2(C)CCCC2)cc1Cl) `ZINC001528669757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528669757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528669757 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2(C)CCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 5, 10, 10, 10, 10, 10, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/389 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2(C)CCCC2)cc1Cl) `ZINC001528669757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528669757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528669757 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2(C)CCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 3, 10, 10, 10, 10, 10, 6, 6, 6, 10, 10, 10, 6, 6, 4, 4, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528669757 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 Building ZINC001528669757 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528669757 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 388) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2(C)CCCC2)cc1Cl) `ZINC001528669757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528669757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528669757 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2(C)CCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 5, 10, 10, 10, 10, 10, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 389) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2(C)CCCC2)cc1Cl) `ZINC001528669757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528669757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528669757 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2(C)CCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 3, 10, 10, 10, 10, 10, 6, 6, 6, 10, 10, 10, 6, 6, 4, 4, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528669757 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528669757 Building ZINC001528683799 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528683799 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/390 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1)c1cccc(C(F)(F)F)c1) `ZINC001528683799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528683799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001528683799 none O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 10, 10, 10, 3, 2, 2, 2, 2, 10, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/391 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1)c1cccc(C(F)(F)F)c1) `ZINC001528683799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528683799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001528683799 none O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 10, 10, 10, 3, 2, 2, 2, 2, 10, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528683799 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 Building ZINC001528683799 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528683799 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 390) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1)c1cccc(C(F)(F)F)c1) `ZINC001528683799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528683799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001528683799 none O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 10, 10, 10, 3, 2, 2, 2, 2, 10, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 391) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1)c1cccc(C(F)(F)F)c1) `ZINC001528683799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528683799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001528683799 none O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 10, 10, 10, 3, 2, 2, 2, 2, 10, 50, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528683799 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528683799 Building ZINC001528684111 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528684111 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/392 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1) `ZINC001528684111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528684111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001528684111 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 6, 6, 5, 6, 6, 4, 8, 8, 8, 8, 8, 8, 20, 20, 38, 39, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 8, 8, 8, 8, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39, 8, 8, 1, 1] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 6, 32, 63, 7, 2, 3, 4, 31, 5, 62, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/393 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1) `ZINC001528684111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528684111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001528684111 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 7, 7, 16, 16, 31, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 1, 1] 40 rigid atoms, others: [0, 1, 34, 35, 36, 33, 6, 32, 63, 7, 2, 3, 4, 31, 5, 62, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528684111 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 Building ZINC001528684111 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528684111 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 392) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1) `ZINC001528684111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528684111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001528684111 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 6, 6, 5, 6, 6, 4, 8, 8, 8, 8, 8, 8, 20, 20, 38, 39, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 8, 8, 8, 8, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39, 8, 8, 1, 1] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 6, 32, 63, 7, 2, 3, 4, 31, 5, 62, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 393) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1) `ZINC001528684111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528684111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001528684111 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 7, 7, 16, 16, 31, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 1, 1] 40 rigid atoms, others: [0, 1, 34, 35, 36, 33, 6, 32, 63, 7, 2, 3, 4, 31, 5, 62, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528684111 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684111 Building ZINC001528684114 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528684114 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/394 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1) `ZINC001528684114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528684114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) Traceback (most recent call last): File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 476, in main() File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 458, in main diff_amsol71_files(atom_list_wat, tot_wat, atom_list_hex, tot_hex, name_wat, numat_wat, outputprefix) File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 273, in diff_amsol71_files Sigmahex[i] = float(atom_listhex[i][5]) # Sigma (kcal/Ang**2) ValueError: could not convert string to float: ******* Solvation calculation failed Skipping ZINC001528684114 0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 `0' -> `0.failed' Finished preparing ZINC001528684114 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Found failed protomers Marking ZINC001528684114 as failed mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/failed' `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114' -> `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114' Building ZINC001528684114 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528684114 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 394) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@H]2CCCN(C(=O)OC(C)(C)C)C2)cc1) `ZINC001528684114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528684114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) Traceback (most recent call last): File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 476, in main() File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 458, in main diff_amsol71_files(atom_list_wat, tot_wat, atom_list_hex, tot_hex, name_wat, numat_wat, outputprefix) File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 273, in diff_amsol71_files Sigmahex[i] = float(atom_listhex[i][5]) # Sigma (kcal/Ang**2) ValueError: could not convert string to float: ******* Solvation calculation failed Skipping ZINC001528684114 0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 `0' -> `0.failed' Finished preparing ZINC001528684114 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Found failed protomers Marking ZINC001528684114 as failed `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528684114' -> `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114' Building ZINC001528802521 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528802521 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/396 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(=O)c1cc(Br)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001528802521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528802521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001528802521 none CCCOC(=O)c1cc(Br)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 15, 15, 7, 15, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 36, 36, 7, 7, 7, 3, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/397 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(=O)c1cc(Br)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001528802521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528802521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001528802521 none CCCOC(=O)c1cc(Br)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 34, 12, 12, 6, 12, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 34, 34, 6, 6, 6, 3, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528802521 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 Building ZINC001528802521 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528802521 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 396) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(=O)c1cc(Br)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001528802521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528802521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001528802521 none CCCOC(=O)c1cc(Br)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 15, 15, 7, 15, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 36, 36, 7, 7, 7, 3, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 397) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(=O)c1cc(Br)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001528802521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528802521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001528802521 none CCCOC(=O)c1cc(Br)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 34, 12, 12, 6, 12, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 39, 39, 39, 39, 39, 34, 34, 6, 6, 6, 3, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528802521 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528802521 Building ZINC001528806618 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528806618 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/398 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1) `ZINC001528806618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528806618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001528806618 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 5, 18, 18, 18, 18, 18, 18, 4, 4, 3, 5, 5, 3, 5, 5, 6, 6, 6, 6, 6, 2, 4, 4, 4, 18, 18, 8, 18, 4, 4, 4, 5, 5, 3, 5, 5] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/399 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1) `ZINC001528806618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528806618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001528806618 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 16, 16, 16, 16, 4, 4, 4, 6, 6, 4, 6, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 16, 16, 4, 16, 4, 4, 4, 6, 6, 4, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528806618 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 Building ZINC001528806618 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528806618 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 398) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1) `ZINC001528806618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528806618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001528806618 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 5, 18, 18, 18, 18, 18, 18, 4, 4, 3, 5, 5, 3, 5, 5, 6, 6, 6, 6, 6, 2, 4, 4, 4, 18, 18, 8, 18, 4, 4, 4, 5, 5, 3, 5, 5] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 399) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1) `ZINC001528806618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528806618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001528806618 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 16, 16, 16, 16, 4, 4, 4, 6, 6, 4, 6, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 16, 16, 4, 16, 4, 4, 4, 6, 6, 4, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528806618 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528806618 Building ZINC001528829384 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528829384 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/400 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528829384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528829384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528829384 none O=C(N(Cc1cccc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 16, 38, 38, 36, 38, 38, 37, 7, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 38, 38, 38, 38, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/401 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528829384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528829384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528829384 none O=C(N(Cc1cccc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 16, 37, 37, 37, 37, 37, 37, 9, 11, 11, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 37, 37, 37, 37, 11, 11, 11, 11, 11, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528829384 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 Building ZINC001528829384 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528829384 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 400) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528829384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528829384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528829384 none O=C(N(Cc1cccc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 16, 38, 38, 36, 38, 38, 37, 7, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 38, 38, 38, 38, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 401) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001528829384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528829384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001528829384 none O=C(N(Cc1cccc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 16, 37, 37, 37, 37, 37, 37, 9, 11, 11, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 37, 37, 37, 37, 11, 11, 11, 11, 11, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528829384 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528829384 Building ZINC001528857525 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528857525 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/402 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2c1cccc2C) `ZINC001528857525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528857525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528857525 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2c1cccc2C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 12, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 4, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 24, 24, 12, 24, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/403 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2c1cccc2C) `ZINC001528857525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528857525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528857525 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2c1cccc2C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 9, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 19, 19, 10, 19, 3, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 65 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528857525 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 Building ZINC001528857525 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528857525 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 402) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2c1cccc2C) `ZINC001528857525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528857525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528857525 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2c1cccc2C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 12, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 4, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 24, 24, 12, 24, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 403) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2c1cccc2C) `ZINC001528857525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528857525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528857525 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2c1cccc2C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 9, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 19, 19, 10, 19, 3, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 65 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528857525 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857525 Building ZINC001528857533 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528857533 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/404 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2c1cccc2C) `ZINC001528857533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528857533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528857533 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2c1cccc2C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 19, 19, 8, 19, 3, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 78 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/405 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2c1cccc2C) `ZINC001528857533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528857533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528857533 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2c1cccc2C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 4, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 4, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 10, 22, 3, 3, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 86 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528857533 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 Building ZINC001528857533 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528857533 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 404) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2c1cccc2C) `ZINC001528857533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528857533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528857533 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2c1cccc2C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 19, 19, 8, 19, 3, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 78 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 405) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2c1cccc2C) `ZINC001528857533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528857533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001528857533 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2c1cccc2C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 4, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 4, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 22, 22, 10, 22, 3, 3, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 86 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528857533 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528857533 Building ZINC001528872600 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528872600 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/406 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/406' -> `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)NCC(C)(C)c1ccc(OCC(C)C)cc1) `ZINC001528872600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528872600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001528872600 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(OCC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 7, 7, 7, 13, 13, 7, 13, 37, 37, 50, 50, 13, 13, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 13, 13, 37, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/407 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/407' -> `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)NCC(C)(C)c1ccc(OCC(C)C)cc1) `ZINC001528872600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528872600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001528872600 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(OCC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 14, 14, 6, 14, 39, 39, 50, 50, 14, 14, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 39, 39, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528872600 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 Building ZINC001528872600 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528872600 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 406) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC(C)(C)c1ccc(OCC(C)C)cc1) `ZINC001528872600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528872600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001528872600 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(OCC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 7, 7, 7, 13, 13, 7, 13, 37, 37, 50, 50, 13, 13, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 13, 13, 37, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 407) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC(C)(C)c1ccc(OCC(C)C)cc1) `ZINC001528872600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528872600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001528872600 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(OCC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 14, 14, 6, 14, 39, 39, 50, 50, 14, 14, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 39, 39, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528872600 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528872600 Building ZINC001528893246 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528893246 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/408 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)cc1) `ZINC001528893246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528893246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001528893246 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 8, 1, 1, 17, 1, 1, 1, 14, 1, 1, 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, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3, 3, 3, 3, 3, 3, 4, 50, 50, 50, 7, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/409 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)cc1) `ZINC001528893246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528893246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001528893246 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 8, 1, 1, 17, 1, 1, 1, 14, 1, 1, 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, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3, 3, 3, 3, 3, 3, 4, 50, 50, 50, 7, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528893246 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 Building ZINC001528893246 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528893246 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 408) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)cc1) `ZINC001528893246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528893246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001528893246 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 8, 1, 1, 17, 1, 1, 1, 14, 1, 1, 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, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3, 3, 3, 3, 3, 3, 4, 50, 50, 50, 7, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 409) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)cc1) `ZINC001528893246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528893246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001528893246 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 8, 1, 1, 17, 1, 1, 1, 14, 1, 1, 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, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3, 3, 3, 3, 3, 3, 4, 50, 50, 50, 7, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528893246 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528893246 Building ZINC001528918865 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528918865 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/410 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(Br)cc(Cl)c32)cc1Cl) `ZINC001528918865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528918865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001528918865 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(Br)cc(Cl)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 10, 4, 10, 10, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 14, 14, 14, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 10] 29 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/411 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(Br)cc(Cl)c32)cc1Cl) `ZINC001528918865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528918865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001528918865 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(Br)cc(Cl)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 2, 10, 10, 1, 1, 1, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 14, 14, 14, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 10] 33 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528918865 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 Building ZINC001528918865 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528918865 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 410) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(Br)cc(Cl)c32)cc1Cl) `ZINC001528918865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528918865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001528918865 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(Br)cc(Cl)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 10, 4, 10, 10, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 14, 14, 14, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 10] 29 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 411) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(Br)cc(Cl)c32)cc1Cl) `ZINC001528918865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528918865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001528918865 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(Br)cc(Cl)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 2, 10, 10, 1, 1, 1, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 14, 14, 14, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 10] 33 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528918865 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528918865 Building ZINC001528991575 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528991575 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/412 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Cn1ccc2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccc21) `ZINC001528991575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528991575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528991575 none CCN(CC)C(=O)Cn1ccc2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 44, 33, 44, 46, 29, 33, 12, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 12, 12, 12, 3, 3, 1, 3, 12, 12] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/413 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Cn1ccc2cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccc21) `ZINC001528991575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528991575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528991575 none CCN(CC)C(=O)Cn1ccc2cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 43, 31, 43, 46, 29, 31, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 11, 11, 11, 2, 3, 1, 3, 11, 11] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528991575 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 Building ZINC001528991575 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528991575 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 412) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Cn1ccc2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccc21) `ZINC001528991575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528991575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528991575 none CCN(CC)C(=O)Cn1ccc2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 44, 33, 44, 46, 29, 33, 12, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 12, 12, 12, 3, 3, 1, 3, 12, 12] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 413) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Cn1ccc2cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccc21) `ZINC001528991575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528991575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001528991575 none CCN(CC)C(=O)Cn1ccc2cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 43, 31, 43, 46, 29, 31, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 11, 11, 11, 2, 3, 1, 3, 11, 11] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/150923/xbj-8058088.36/working/building/ZINC001528991575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528991575 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528991575 Building ZINC001528992222 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528992222 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/414 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001528992222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528992222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001528992222 none COc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 14, 15, 15, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 17, 17, 10, 17, 17, 21, 21, 21, 15, 15, 15, 15, 4, 9, 9, 17, 17, 10, 17, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/415 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001528992222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528992222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001528992222 none COc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 19, 11, 19, 19, 9, 5, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 9, 17, 17, 11, 17, 17, 26, 26, 26, 19, 19, 19, 19, 5, 8, 8, 17, 17, 14, 17, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528992222 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 Building ZINC001528992222 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528992222 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 414) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001528992222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528992222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001528992222 none COc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 14, 15, 15, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 17, 17, 10, 17, 17, 21, 21, 21, 15, 15, 15, 15, 4, 9, 9, 17, 17, 10, 17, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 415) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001528992222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528992222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001528992222 none COc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 19, 11, 19, 19, 9, 5, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 9, 17, 17, 11, 17, 17, 26, 26, 26, 19, 19, 19, 19, 5, 8, 8, 17, 17, 14, 17, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528992222 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992222 Building ZINC001528992226 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528992226 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/416 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001528992226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528992226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001528992226 none COc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 11, 18, 18, 9, 5, 9, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 10, 17, 17, 25, 25, 25, 18, 18, 18, 18, 5, 9, 9, 17, 17, 17, 17, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/417 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001528992226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528992226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001528992226 none COc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 9, 15, 15, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 16, 16, 9, 16, 16, 21, 21, 21, 15, 15, 15, 15, 4, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528992226 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 Building ZINC001528992226 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001528992226 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 416) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001528992226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001528992226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001528992226 none COc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 11, 18, 18, 9, 5, 9, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 10, 17, 17, 25, 25, 25, 18, 18, 18, 18, 5, 9, 9, 17, 17, 17, 17, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 417) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001528992226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001528992226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001528992226 none COc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 9, 15, 15, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 16, 16, 9, 16, 16, 21, 21, 21, 15, 15, 15, 15, 4, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001528992226 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001528992226 Building ZINC001529030861 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529030861 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/418 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(C(C)(C)C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529030861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529030861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529030861 none CCOC(=O)c1cc(C(C)(C)C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 5, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 15, 7, 15, 7, 7, 7, 7, 13, 13, 13, 7, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/419 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(C(C)(C)C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529030861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529030861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529030861 none CCOC(=O)c1cc(C(C)(C)C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 5, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 15, 7, 15, 7, 7, 7, 7, 13, 13, 13, 7, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529030861 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 Building ZINC001529030861 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529030861 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 418) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(C(C)(C)C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529030861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529030861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529030861 none CCOC(=O)c1cc(C(C)(C)C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 5, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 15, 7, 15, 7, 7, 7, 7, 13, 13, 13, 7, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 419) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(C(C)(C)C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529030861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529030861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529030861 none CCOC(=O)c1cc(C(C)(C)C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 5, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 15, 7, 15, 7, 7, 7, 7, 13, 13, 13, 7, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529030861 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529030861 Building ZINC001529050246 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529050246 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/420 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529050246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529050246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001529050246 none O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 10, 12, 12, 12, 12, 12, 18, 21, 44, 44, 44, 44, 44, 44, 44, 12, 1, 1, 1, 4, 4, 4, 4, 4, 2, 8, 8, 10, 10, 12, 12, 12, 21, 21, 44, 44, 44, 44, 44, 44, 44, 44, 44, 12, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/421 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529050246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529050246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001529050246 none O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 10, 12, 12, 12, 12, 12, 18, 21, 44, 44, 44, 44, 44, 44, 44, 12, 1, 1, 1, 4, 4, 4, 4, 4, 2, 8, 8, 10, 10, 12, 12, 12, 21, 21, 44, 44, 44, 44, 44, 44, 44, 44, 44, 12, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529050246 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 Building ZINC001529050246 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529050246 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 420) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529050246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529050246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001529050246 none O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 10, 12, 12, 12, 12, 12, 18, 21, 44, 44, 44, 44, 44, 44, 44, 12, 1, 1, 1, 4, 4, 4, 4, 4, 2, 8, 8, 10, 10, 12, 12, 12, 21, 21, 44, 44, 44, 44, 44, 44, 44, 44, 44, 12, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 421) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529050246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529050246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001529050246 none O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 10, 12, 12, 12, 12, 12, 18, 21, 44, 44, 44, 44, 44, 44, 44, 12, 1, 1, 1, 4, 4, 4, 4, 4, 2, 8, 8, 10, 10, 12, 12, 12, 21, 21, 44, 44, 44, 44, 44, 44, 44, 44, 44, 12, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529050246 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529050246 Building ZINC001529063856 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529063856 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/422 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccc(Cl)nn2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529063856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529063856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529063856 none O=C(Nc1ccc(Oc2ccc(Cl)nn2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 24, 41, 41, 41, 41, 41, 41, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 4, 4, 41, 41, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/423 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccc(Cl)nn2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529063856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529063856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529063856 none O=C(Nc1ccc(Oc2ccc(Cl)nn2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 2, 24, 41, 41, 41, 41, 41, 41, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 4, 4, 41, 41, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529063856 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 Building ZINC001529063856 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529063856 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 422) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccc(Cl)nn2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529063856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529063856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529063856 none O=C(Nc1ccc(Oc2ccc(Cl)nn2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 24, 41, 41, 41, 41, 41, 41, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 4, 4, 41, 41, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 423) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccc(Cl)nn2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529063856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529063856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529063856 none O=C(Nc1ccc(Oc2ccc(Cl)nn2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 2, 24, 41, 41, 41, 41, 41, 41, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 4, 4, 41, 41, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529063856 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529063856 Building ZINC001529065703 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529065703 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/424 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccccc1C) `ZINC001529065703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529065703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529065703 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 9, 14, 14, 9, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 6, 9, 9, 14, 14, 9, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/425 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccccc1C) `ZINC001529065703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529065703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529065703 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 10, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 4, 12, 3, 3, 3, 2, 6, 6, 6, 10, 10, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529065703 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 Building ZINC001529065703 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529065703 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 424) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccccc1C) `ZINC001529065703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529065703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529065703 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 9, 14, 14, 9, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 6, 9, 9, 14, 14, 9, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 425) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccccc1C) `ZINC001529065703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529065703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529065703 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1ccccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 10, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 4, 12, 3, 3, 3, 2, 6, 6, 6, 10, 10, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529065703 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065703 Building ZINC001529065704 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529065704 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/426 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccccc1C) `ZINC001529065704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529065704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529065704 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 10, 13, 13, 13, 13, 13, 13, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 5, 5, 5, 10, 10, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/427 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccccc1C) `ZINC001529065704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529065704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529065704 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 9, 14, 14, 14, 14, 14, 14, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 5, 5, 5, 9, 9, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529065704 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 Building ZINC001529065704 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529065704 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 426) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccccc1C) `ZINC001529065704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529065704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529065704 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 10, 13, 13, 13, 13, 13, 13, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 5, 5, 5, 10, 10, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 427) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccccc1C) `ZINC001529065704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529065704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529065704 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1ccccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 9, 14, 14, 14, 14, 14, 14, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 5, 5, 5, 9, 9, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529065704 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529065704 Building ZINC001529086635 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529086635 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/428 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1N1CCCCC1) `ZINC001529086635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529086635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001529086635 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 40, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 18, 35, 35, 35, 35, 35, 40, 40, 40, 14, 2, 3, 1, 3, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/429 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1N1CCCCC1) `ZINC001529086635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529086635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001529086635 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 14, 41, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 17, 34, 34, 34, 34, 34, 41, 41, 41, 14, 2, 3, 1, 3, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529086635 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 Building ZINC001529086635 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529086635 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 428) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1N1CCCCC1) `ZINC001529086635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529086635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001529086635 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 40, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 18, 35, 35, 35, 35, 35, 40, 40, 40, 14, 2, 3, 1, 3, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 429) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1N1CCCCC1) `ZINC001529086635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529086635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001529086635 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 14, 41, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 17, 34, 34, 34, 34, 34, 41, 41, 41, 14, 2, 3, 1, 3, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529086635 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529086635 Building ZINC001529090239 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529090239 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/430 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)OC(C)(C)C)cccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529090239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529090239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001529090239 none Cc1c(NC(=O)OC(C)(C)C)cccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 22, 29, 29, 37, 37, 37, 37, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 3, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/431 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)OC(C)(C)C)cccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529090239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529090239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001529090239 none Cc1c(NC(=O)OC(C)(C)C)cccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 21, 28, 28, 37, 37, 37, 37, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 3, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529090239 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 Building ZINC001529090239 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529090239 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 430) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)OC(C)(C)C)cccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529090239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529090239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001529090239 none Cc1c(NC(=O)OC(C)(C)C)cccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 22, 29, 29, 37, 37, 37, 37, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 3, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 431) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)OC(C)(C)C)cccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529090239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529090239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001529090239 none Cc1c(NC(=O)OC(C)(C)C)cccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 21, 28, 28, 37, 37, 37, 37, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 3, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529090239 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529090239 Building ZINC001529163097 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529163097 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/432 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)c(C)c2)CCCCC1) `ZINC001529163097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529163097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529163097 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)c(C)c2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 10, 19, 42, 42, 42, 42, 42, 42, 42, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 6, 42, 42, 42, 42, 42, 42, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/433 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)c(C)c2)CCCCC1) `ZINC001529163097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529163097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529163097 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)c(C)c2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 10, 18, 44, 44, 38, 44, 44, 44, 44, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 6, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529163097 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 Building ZINC001529163097 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529163097 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 432) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)c(C)c2)CCCCC1) `ZINC001529163097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529163097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529163097 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)c(C)c2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 10, 19, 42, 42, 42, 42, 42, 42, 42, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 6, 42, 42, 42, 42, 42, 42, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 433) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)c(C)c2)CCCCC1) `ZINC001529163097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529163097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529163097 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)c(C)c2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 10, 18, 44, 44, 38, 44, 44, 44, 44, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 6, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529163097 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529163097 Building ZINC001529185686 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529185686 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/434 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(C)c(C)n2c1ccc(Cl)cc1) `ZINC001529185686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529185686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001529185686 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(C)c(C)n2c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 39, 39, 27, 27, 39, 39, 10, 10, 10, 8, 8, 8, 8, 7, 27, 27, 27, 27, 27, 27, 27, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/435 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(C)c(C)n2c1ccc(Cl)cc1) `ZINC001529185686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529185686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001529185686 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(C)c(C)n2c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 39, 39, 27, 27, 39, 39, 10, 10, 10, 8, 8, 8, 8, 7, 27, 27, 27, 27, 27, 27, 27, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529185686 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 Building ZINC001529185686 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529185686 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 434) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ncnc2c1c(C)c(C)n2c1ccc(Cl)cc1) `ZINC001529185686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529185686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001529185686 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(C)c(C)n2c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 39, 39, 27, 27, 39, 39, 10, 10, 10, 8, 8, 8, 8, 7, 27, 27, 27, 27, 27, 27, 27, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 435) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ncnc2c1c(C)c(C)n2c1ccc(Cl)cc1) `ZINC001529185686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529185686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001529185686 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(C)c(C)n2c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 39, 39, 27, 27, 39, 39, 10, 10, 10, 8, 8, 8, 8, 7, 27, 27, 27, 27, 27, 27, 27, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529185686 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529185686 Building ZINC001529190844 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529190844 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/436 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2ccc(C)cc21) `ZINC001529190844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529190844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001529190844 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2ccc(C)cc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 23, 23, 8, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 3, 7, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 23, 23, 15, 23, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/437 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2ccc(C)cc21) `ZINC001529190844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529190844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001529190844 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2ccc(C)cc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 3, 6, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 76 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529190844 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 Building ZINC001529190844 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529190844 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 436) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2ccc(C)cc21) `ZINC001529190844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529190844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001529190844 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2ccc(C)cc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 23, 23, 8, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 3, 7, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 23, 23, 15, 23, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 437) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2ccc(C)cc21) `ZINC001529190844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529190844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001529190844 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2ccc(C)cc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 3, 6, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 76 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529190844 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529190844 Building ZINC001529238106 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529238106 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/438 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(Cc3ccc(Br)cc3)CCCCC2)cn1) `ZINC001529238106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529238106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529238106 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(Cc3ccc(Br)cc3)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 4, 4, 6, 8, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/439 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(Cc3ccc(Br)cc3)CCCCC2)cn1) `ZINC001529238106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529238106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529238106 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(Cc3ccc(Br)cc3)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 7, 1, 1, 1, 1, 4, 4, 6, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 4, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529238106 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 Building ZINC001529238106 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529238106 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 438) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(Cc3ccc(Br)cc3)CCCCC2)cn1) `ZINC001529238106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529238106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529238106 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(Cc3ccc(Br)cc3)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 4, 4, 6, 8, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 439) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(Cc3ccc(Br)cc3)CCCCC2)cn1) `ZINC001529238106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529238106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529238106 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(Cc3ccc(Br)cc3)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 7, 1, 1, 1, 1, 4, 4, 6, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 4, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529238106 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238106 Building ZINC001529238804 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529238804 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/440 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)c2ccccc21) `ZINC001529238804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529238804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529238804 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)c2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 13, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 13, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/441 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)c2ccccc21) `ZINC001529238804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529238804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529238804 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)c2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529238804 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 Building ZINC001529238804 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529238804 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 440) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)c2ccccc21) `ZINC001529238804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529238804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529238804 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)c2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 13, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 13, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 441) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)c2ccccc21) `ZINC001529238804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529238804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529238804 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)c2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529238804 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238804 Building ZINC001529238805 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529238805 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/442 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)c2ccccc21) `ZINC001529238805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529238805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529238805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)c2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/443 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)c2ccccc21) `ZINC001529238805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529238805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529238805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)c2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 23, 23, 3, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 23, 23, 3, 23, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529238805 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 Building ZINC001529238805 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529238805 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 442) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)c2ccccc21) `ZINC001529238805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529238805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529238805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)c2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 443) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)c2ccccc21) `ZINC001529238805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529238805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529238805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)c2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 23, 23, 3, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 23, 23, 3, 23, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529238805 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529238805 Building ZINC001529256448 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529256448 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/444 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)cc1) `ZINC001529256448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529256448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001529256448 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 28, 37, 37, 33, 37, 37, 37, 37, 37, 37, 28, 28, 28, 28, 28, 28, 13, 13, 2, 6, 6, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/445 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)cc1) `ZINC001529256448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529256448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001529256448 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 6, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529256448 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 Building ZINC001529256448 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529256448 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 444) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)cc1) `ZINC001529256448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529256448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001529256448 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 28, 37, 37, 33, 37, 37, 37, 37, 37, 37, 28, 28, 28, 28, 28, 28, 13, 13, 2, 6, 6, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 445) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)cc1) `ZINC001529256448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529256448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001529256448 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 6, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529256448 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529256448 Building ZINC001529291911 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529291911 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/446 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccnc(Cl)n2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529291911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529291911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529291911 none O=C(Nc1ccc(Oc2ccnc(Cl)n2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 16, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 23, 42, 42, 42, 42, 42, 42, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 4, 4, 42, 42, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/447 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccnc(Cl)n2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529291911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529291911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529291911 none O=C(Nc1ccc(Oc2ccnc(Cl)n2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 16, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 2, 23, 42, 42, 42, 42, 42, 42, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 4, 4, 42, 42, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529291911 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 Building ZINC001529291911 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529291911 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 446) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccnc(Cl)n2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529291911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529291911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529291911 none O=C(Nc1ccc(Oc2ccnc(Cl)n2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 16, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 4, 23, 42, 42, 42, 42, 42, 42, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 4, 4, 42, 42, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 447) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccnc(Cl)n2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529291911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529291911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529291911 none O=C(Nc1ccc(Oc2ccnc(Cl)n2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 16, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 2, 2, 23, 42, 42, 42, 42, 42, 42, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 4, 4, 42, 42, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529291911 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529291911 Building ZINC001529309850 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529309850 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/448 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)c(Br)c1) `ZINC001529309850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529309850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529309850 none Cc1ccc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 12, 12, 12, 9, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 4, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/449 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)c(Br)c1) `ZINC001529309850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529309850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529309850 none Cc1ccc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529309850 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 Building ZINC001529309850 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529309850 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 448) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)c(Br)c1) `ZINC001529309850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529309850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529309850 none Cc1ccc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 12, 12, 12, 9, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 4, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 449) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)c(Br)c1) `ZINC001529309850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529309850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001529309850 none Cc1ccc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529309850 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529309850 Building ZINC001529338047 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529338047 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/450 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccs1) `ZINC001529338047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529338047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529338047 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 10, 11, 11, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 7, 7, 11, 11, 11, 11, 11, 11, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/451 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccs1) `ZINC001529338047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529338047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529338047 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 9, 10, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 10, 10, 10, 10, 10, 10, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529338047 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 Building ZINC001529338047 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529338047 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 450) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccs1) `ZINC001529338047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529338047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529338047 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 10, 11, 11, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 7, 7, 11, 11, 11, 11, 11, 11, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 451) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccs1) `ZINC001529338047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529338047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529338047 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 9, 10, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 10, 10, 10, 10, 10, 10, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529338047 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529338047 Building ZINC001529352629 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529352629 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/452 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Oc2ccc(Cl)cc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001529352629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529352629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001529352629 none COC(=O)c1cc(Oc2ccc(Cl)cc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 8, 7, 7, 7, 7, 40, 50, 50, 40, 50, 50, 50, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 7, 50, 50, 50, 50, 7, 7, 3, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/453 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Oc2ccc(Cl)cc2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001529352629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529352629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001529352629 none COC(=O)c1cc(Oc2ccc(Cl)cc2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 8, 7, 7, 7, 7, 40, 50, 50, 40, 50, 50, 50, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 7, 50, 50, 50, 50, 7, 7, 3, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529352629 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 Building ZINC001529352629 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529352629 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 452) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Oc2ccc(Cl)cc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001529352629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529352629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001529352629 none COC(=O)c1cc(Oc2ccc(Cl)cc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 8, 7, 7, 7, 7, 40, 50, 50, 40, 50, 50, 50, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 7, 50, 50, 50, 50, 7, 7, 3, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 453) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Oc2ccc(Cl)cc2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001529352629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529352629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001529352629 none COC(=O)c1cc(Oc2ccc(Cl)cc2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 8, 7, 7, 7, 7, 40, 50, 50, 40, 50, 50, 50, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 7, 50, 50, 50, 50, 7, 7, 3, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529352629 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529352629 Building ZINC001529359762 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529359762 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/454 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(Cc2cnc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)s2)c1) `ZINC001529359762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529359762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529359762 none COC(=O)c1cccc(Cc2cnc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 31, 31, 31, 16, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 31, 50, 50, 50, 31, 31, 31, 16, 16, 4, 2, 2, 1, 2, 31] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/455 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(Cc2cnc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)s2)c1) `ZINC001529359762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529359762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529359762 none COC(=O)c1cccc(Cc2cnc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 31, 31, 31, 16, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 31, 50, 50, 50, 31, 31, 31, 16, 16, 4, 2, 2, 1, 2, 31] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529359762 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 Building ZINC001529359762 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529359762 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 454) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(Cc2cnc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)s2)c1) `ZINC001529359762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529359762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529359762 none COC(=O)c1cccc(Cc2cnc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 31, 31, 31, 16, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 31, 50, 50, 50, 31, 31, 31, 16, 16, 4, 2, 2, 1, 2, 31] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 455) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(Cc2cnc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)s2)c1) `ZINC001529359762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529359762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529359762 none COC(=O)c1cccc(Cc2cnc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 31, 31, 31, 16, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 31, 50, 50, 50, 31, 31, 31, 16, 16, 4, 2, 2, 1, 2, 31] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529359762 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529359762 Building ZINC001529380028 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529380028 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/456 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001529380028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529380028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001529380028 none CC(C)(C)OC(=O)N[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 18, 29, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 18, 7, 7, 7, 7, 7, 7, 3, 1, 3, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/457 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001529380028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529380028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001529380028 none CC(C)(C)OC(=O)N[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 19, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 9, 9, 9, 9, 9, 9, 3, 1, 3, 9, 9] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529380028 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028 Building ZINC001529380028 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529380028 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 456) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001529380028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529380028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001529380028 none CC(C)(C)OC(=O)N[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 18, 29, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 47, 47, 47, 47, 47, 47, 47, 47, 47, 18, 7, 7, 7, 7, 7, 7, 3, 1, 3, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 457) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001529380028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529380028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001529380028 none CC(C)(C)OC(=O)N[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 19, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 9, 9, 9, 9, 9, 9, 3, 1, 3, 9, 9] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/150923/xbj-8058088.36/working/building/ZINC001529380028 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529380028 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380028 Building ZINC001529380032 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529380032 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/458 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001529380032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529380032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001529380032 none CC(C)(C)OC(=O)N[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 19, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 3, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 10, 10, 10, 10, 10, 10, 3, 1, 3, 10, 10] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/459 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001529380032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529380032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001529380032 none CC(C)(C)OC(=O)N[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 20, 30, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 7, 7, 7, 7, 7, 7, 3, 1, 3, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529380032 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 Building ZINC001529380032 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529380032 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 458) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001529380032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529380032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001529380032 none CC(C)(C)OC(=O)N[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 19, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 3, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 10, 10, 10, 10, 10, 10, 3, 1, 3, 10, 10] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 459) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001529380032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529380032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001529380032 none CC(C)(C)OC(=O)N[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 20, 30, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 7, 7, 7, 7, 7, 7, 3, 1, 3, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529380032 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529380032 Building ZINC001529426491 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529426491 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/460 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(C)c(OCc2cccc(C)c2)c(C)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001529426491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529426491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001529426491 none CCN(Cc1cc(C)c(OCc2cccc(C)c2)c(C)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 8, 16, 39, 39, 30, 39, 39, 39, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 39, 39, 30, 39, 39, 39, 39, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 37, 38, 33, 2, 3, 25, 21, 22, 23, 24, 36, 4] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/461 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(C)c(OCc2cccc(C)c2)c(C)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001529426491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529426491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001529426491 none CCN(Cc1cc(C)c(OCc2cccc(C)c2)c(C)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 2, 7, 15, 38, 38, 29, 38, 38, 38, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 15, 38, 38, 29, 38, 38, 38, 38, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 37, 38, 33, 2, 3, 25, 21, 22, 23, 24, 36, 4] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529426491 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 Building ZINC001529426491 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529426491 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 460) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cc1cc(C)c(OCc2cccc(C)c2)c(C)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001529426491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529426491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001529426491 none CCN(Cc1cc(C)c(OCc2cccc(C)c2)c(C)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 8, 16, 39, 39, 30, 39, 39, 39, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 39, 39, 30, 39, 39, 39, 39, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 37, 38, 33, 2, 3, 25, 21, 22, 23, 24, 36, 4] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 461) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cc1cc(C)c(OCc2cccc(C)c2)c(C)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001529426491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529426491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001529426491 none CCN(Cc1cc(C)c(OCc2cccc(C)c2)c(C)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 2, 7, 15, 38, 38, 29, 38, 38, 38, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 15, 38, 38, 29, 38, 38, 38, 38, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 37, 38, 33, 2, 3, 25, 21, 22, 23, 24, 36, 4] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529426491 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529426491 Building ZINC001529452293 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529452293 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/462 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C) `ZINC001529452293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529452293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452293 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 40, 40, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/463 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C) `ZINC001529452293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529452293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452293 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 17, 18, 41, 41, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529452293 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 Building ZINC001529452293 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529452293 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 462) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C) `ZINC001529452293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529452293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452293 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 40, 40, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 463) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C) `ZINC001529452293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529452293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452293 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 17, 18, 41, 41, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529452293 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452293 Building ZINC001529452294 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529452294 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/464 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C) `ZINC001529452294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529452294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452294 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 17, 10, 10, 10, 38, 38, 49, 49, 50, 49, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 4, 49, 49, 49, 50, 50, 50, 50, 49, 49, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/465 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C) `ZINC001529452294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529452294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452294 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 15, 10, 10, 10, 38, 38, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529452294 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 Building ZINC001529452294 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529452294 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 464) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C) `ZINC001529452294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529452294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452294 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 17, 10, 10, 10, 38, 38, 49, 49, 50, 49, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 4, 49, 49, 49, 50, 50, 50, 50, 49, 49, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 465) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C) `ZINC001529452294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529452294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452294 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 15, 10, 10, 10, 38, 38, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529452294 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452294 Building ZINC001529452295 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529452295 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/466 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C) `ZINC001529452295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529452295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452295 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 15, 10, 10, 10, 41, 42, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/467 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C) `ZINC001529452295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529452295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452295 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 17, 10, 10, 10, 36, 40, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529452295 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 Building ZINC001529452295 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529452295 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 466) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C) `ZINC001529452295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529452295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452295 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 15, 10, 10, 10, 41, 42, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 467) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C) `ZINC001529452295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529452295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452295 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 17, 10, 10, 10, 36, 40, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529452295 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452295 Building ZINC001529452296 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529452296 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/468 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C) `ZINC001529452296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529452296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452296 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 41, 41, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/469 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C) `ZINC001529452296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529452296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452296 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 17, 18, 40, 40, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529452296 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 Building ZINC001529452296 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529452296 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 468) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C) `ZINC001529452296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529452296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452296 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 41, 41, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 469) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C) `ZINC001529452296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529452296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001529452296 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 17, 18, 40, 40, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529452296 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529452296 Building ZINC001529515884 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529515884 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/470 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC[C@H](Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529515884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529515884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001529515884 none CCCOC[C@H](Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 17, 8, 6, 2, 6, 6, 11, 18, 18, 18, 18, 18, 18, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 24, 24, 8, 8, 11, 11, 18, 18, 18, 18, 2, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/471 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC[C@H](Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529515884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529515884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001529515884 none CCCOC[C@H](Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 6, 2, 6, 6, 12, 19, 19, 19, 19, 19, 19, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 19, 19, 8, 8, 12, 12, 19, 19, 19, 19, 2, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529515884 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 Building ZINC001529515884 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529515884 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 470) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC[C@H](Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529515884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529515884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001529515884 none CCCOC[C@H](Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 17, 8, 6, 2, 6, 6, 11, 18, 18, 18, 18, 18, 18, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 24, 24, 8, 8, 11, 11, 18, 18, 18, 18, 2, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 471) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC[C@H](Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529515884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529515884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001529515884 none CCCOC[C@H](Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 6, 2, 6, 6, 12, 19, 19, 19, 19, 19, 19, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 19, 19, 8, 8, 12, 12, 19, 19, 19, 19, 2, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529515884 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515884 Building ZINC001529515885 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529515885 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/472 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC[C@@H](Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529515885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529515885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001529515885 none CCCOC[C@@H](Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 8, 6, 2, 6, 6, 12, 19, 19, 19, 19, 19, 19, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 20, 20, 8, 8, 12, 12, 19, 19, 19, 19, 2, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/473 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC[C@@H](Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529515885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529515885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001529515885 none CCCOC[C@@H](Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 17, 8, 6, 2, 6, 6, 11, 18, 18, 18, 18, 18, 18, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 24, 24, 8, 8, 11, 11, 18, 18, 18, 18, 2, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529515885 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 Building ZINC001529515885 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529515885 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 472) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC[C@@H](Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529515885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529515885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001529515885 none CCCOC[C@@H](Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 8, 6, 2, 6, 6, 12, 19, 19, 19, 19, 19, 19, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 20, 20, 8, 8, 12, 12, 19, 19, 19, 19, 2, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 473) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC[C@@H](Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529515885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529515885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001529515885 none CCCOC[C@@H](Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 17, 8, 6, 2, 6, 6, 11, 18, 18, 18, 18, 18, 18, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 24, 24, 8, 8, 11, 11, 18, 18, 18, 18, 2, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529515885 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529515885 Building ZINC001529517624 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529517624 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/474 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccs1) `ZINC001529517624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529517624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001529517624 none O=C(Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 13, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 20, 35, 35, 35, 35, 20, 13, 13, 13, 13, 4, 7, 7, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/475 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccs1) `ZINC001529517624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529517624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001529517624 none O=C(Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 13, 13, 13, 10, 13, 13, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 20, 35, 35, 35, 35, 20, 13, 13, 13, 13, 4, 7, 7, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529517624 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 Building ZINC001529517624 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529517624 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 474) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccs1) `ZINC001529517624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529517624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001529517624 none O=C(Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 13, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 20, 35, 35, 35, 35, 20, 13, 13, 13, 13, 4, 7, 7, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 475) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccs1) `ZINC001529517624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529517624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001529517624 none O=C(Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 13, 13, 13, 10, 13, 13, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 20, 35, 35, 35, 35, 20, 13, 13, 13, 13, 4, 7, 7, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529517624 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529517624 Building ZINC001529580891 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529580891 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/476 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529580891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529580891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001529580891 none C[C@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 4, 2, 5, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 11, 11, 11, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 6, 13, 13, 6, 13, 13, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/477 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529580891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529580891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001529580891 none C[C@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 5, 2, 7, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 14, 14, 14, 25, 25, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 5, 9, 9, 5, 9, 9, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529580891 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 Building ZINC001529580891 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529580891 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 476) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529580891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529580891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001529580891 none C[C@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 4, 2, 5, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 11, 11, 11, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 6, 13, 13, 6, 13, 13, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 477) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529580891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529580891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001529580891 none C[C@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 5, 2, 7, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 14, 14, 14, 25, 25, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 5, 9, 9, 5, 9, 9, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529580891 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580891 Building ZINC001529580893 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529580893 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/478 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529580893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529580893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001529580893 none C[C@@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 5, 2, 7, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 14, 14, 14, 25, 25, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 5, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/479 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529580893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529580893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001529580893 none C[C@@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 4, 2, 5, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 11, 11, 11, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 6, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529580893 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 Building ZINC001529580893 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529580893 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 478) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529580893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529580893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001529580893 none C[C@@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 5, 2, 7, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 14, 14, 14, 25, 25, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 5, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 479) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529580893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529580893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001529580893 none C[C@@]1(Cc2ccccc2C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 4, 2, 5, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 11, 11, 11, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 6, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529580893 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529580893 Building ZINC001529596628 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529596628 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/480 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(N(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001529596628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529596628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529596628 none CN(C)c1ccc(N(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 19, 9, 9, 9, 9, 4, 9, 19, 30, 30, 30, 30, 30, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 9, 9, 19, 19, 19, 19, 19, 19, 9, 9, 19, 19, 30, 30, 30, 30, 4, 2, 4, 9, 9] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/481 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(N(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001529596628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529596628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529596628 none CN(C)c1ccc(N(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 9, 10, 10, 9, 4, 9, 19, 30, 30, 30, 30, 30, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 10, 10, 20, 20, 20, 20, 20, 20, 10, 10, 19, 19, 30, 30, 30, 30, 4, 1, 4, 10, 10] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529596628 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 Building ZINC001529596628 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529596628 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 480) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(N(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001529596628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529596628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529596628 none CN(C)c1ccc(N(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 19, 9, 9, 9, 9, 4, 9, 19, 30, 30, 30, 30, 30, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 9, 9, 19, 19, 19, 19, 19, 19, 9, 9, 19, 19, 30, 30, 30, 30, 4, 2, 4, 9, 9] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 481) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(N(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001529596628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529596628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001529596628 none CN(C)c1ccc(N(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 9, 10, 10, 9, 4, 9, 19, 30, 30, 30, 30, 30, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 10, 10, 20, 20, 20, 20, 20, 20, 10, 10, 19, 19, 30, 30, 30, 30, 4, 1, 4, 10, 10] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/150923/xbj-8058088.36/working/building/ZINC001529596628 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529596628 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529596628 Building ZINC001529602161 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529602161 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/482 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cc(Br)cs2)cs1) `ZINC001529602161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529602161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529602161 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cc(Br)cs2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 14, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 45, 45, 45, 45, 45, 8, 8, 3, 3, 3, 3, 3, 3, 4, 45, 45, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/483 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cc(Br)cs2)cs1) `ZINC001529602161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529602161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529602161 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cc(Br)cs2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 14, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 45, 45, 45, 45, 45, 8, 8, 3, 3, 3, 3, 3, 3, 4, 45, 45, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529602161 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 Building ZINC001529602161 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529602161 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 482) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cc(Br)cs2)cs1) `ZINC001529602161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529602161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529602161 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cc(Br)cs2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 14, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 45, 45, 45, 45, 45, 8, 8, 3, 3, 3, 3, 3, 3, 4, 45, 45, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 483) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cc(Br)cs2)cs1) `ZINC001529602161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529602161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001529602161 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cc(Br)cs2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 14, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 45, 45, 45, 45, 45, 8, 8, 3, 3, 3, 3, 3, 3, 4, 45, 45, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529602161 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529602161 Building ZINC001529611640 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529611640 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/484 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccccc3OC)cc2)cc1Cl) `ZINC001529611640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529611640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001529611640 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccccc3OC)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 8, 10, 25, 25, 25, 25, 25, 25, 25, 29, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 10, 10, 25, 25, 25, 25, 29, 29, 29, 10, 10, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/485 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccccc3OC)cc2)cc1Cl) `ZINC001529611640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529611640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001529611640 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccccc3OC)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 6, 5, 25, 25, 25, 25, 25, 25, 25, 29, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 10, 10, 25, 25, 25, 25, 29, 29, 29, 10, 10, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529611640 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 Building ZINC001529611640 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529611640 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 484) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccccc3OC)cc2)cc1Cl) `ZINC001529611640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529611640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001529611640 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccccc3OC)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 8, 10, 25, 25, 25, 25, 25, 25, 25, 29, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 10, 10, 25, 25, 25, 25, 29, 29, 29, 10, 10, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 485) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccccc3OC)cc2)cc1Cl) `ZINC001529611640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529611640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001529611640 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccccc3OC)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 6, 5, 25, 25, 25, 25, 25, 25, 25, 29, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 10, 10, 25, 25, 25, 25, 29, 29, 29, 10, 10, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529611640 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529611640 Building ZINC001529613404 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529613404 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/486 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/486' -> `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)N1CCCc2c(C)c(F)cc(Cl)c21) `ZINC001529613404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529613404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529613404 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(C)c(F)cc(Cl)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 1, 15, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 12 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 28 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/487 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/487' -> `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)N1CCCc2c(C)c(F)cc(Cl)c21) `ZINC001529613404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529613404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529613404 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(C)c(F)cc(Cl)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 1, 15, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 5, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 14 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 36 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529613404 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 Building ZINC001529613404 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529613404 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 486) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCCc2c(C)c(F)cc(Cl)c21) `ZINC001529613404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529613404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529613404 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(C)c(F)cc(Cl)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 1, 15, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 12 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 28 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 487) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCCc2c(C)c(F)cc(Cl)c21) `ZINC001529613404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529613404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529613404 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(C)c(F)cc(Cl)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 1, 15, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 5, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 14 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 36 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529613404 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529613404 Building ZINC001529622240 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529622240 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/488 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OCc3cccc(F)c3)cc2)cc1Cl) `ZINC001529622240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529622240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001529622240 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OCc3cccc(F)c3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 4, 8, 8, 29, 29, 29, 29, 29, 29, 6, 6, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 6, 6, 8, 8, 29, 29, 29, 29, 6, 6, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/489 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OCc3cccc(F)c3)cc2)cc1Cl) `ZINC001529622240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529622240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001529622240 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OCc3cccc(F)c3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 5, 8, 8, 29, 29, 29, 29, 29, 29, 6, 6, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 6, 6, 8, 8, 29, 29, 29, 29, 6, 6, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529622240 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 Building ZINC001529622240 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529622240 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 488) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OCc3cccc(F)c3)cc2)cc1Cl) `ZINC001529622240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529622240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001529622240 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OCc3cccc(F)c3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 4, 8, 8, 29, 29, 29, 29, 29, 29, 6, 6, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 6, 6, 8, 8, 29, 29, 29, 29, 6, 6, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 489) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OCc3cccc(F)c3)cc2)cc1Cl) `ZINC001529622240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529622240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001529622240 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OCc3cccc(F)c3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 5, 8, 8, 29, 29, 29, 29, 29, 29, 6, 6, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 6, 6, 8, 8, 29, 29, 29, 29, 6, 6, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529622240 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529622240 Building ZINC001529635243 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529635243 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/490 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc(c2ccc(Cl)s2)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529635243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529635243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001529635243 none O=C(Nc1cnc(c2ccc(Cl)s2)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 16, 14, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 8, 8, 38, 38, 38, 38, 38, 9, 9, 1, 1, 1, 10, 10, 10, 10, 10, 4, 9, 38, 38, 9, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/491 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc(c2ccc(Cl)s2)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529635243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529635243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001529635243 none O=C(Nc1cnc(c2ccc(Cl)s2)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 16, 14, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 4, 4, 26, 37, 40, 40, 26, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 4, 10, 26, 40, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529635243 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 Building ZINC001529635243 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529635243 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 490) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc(c2ccc(Cl)s2)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529635243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529635243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001529635243 none O=C(Nc1cnc(c2ccc(Cl)s2)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 16, 14, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 8, 8, 38, 38, 38, 38, 38, 9, 9, 1, 1, 1, 10, 10, 10, 10, 10, 4, 9, 38, 38, 9, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 491) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc(c2ccc(Cl)s2)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529635243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529635243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001529635243 none O=C(Nc1cnc(c2ccc(Cl)s2)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 16, 14, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 4, 4, 26, 37, 40, 40, 26, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 4, 10, 26, 40, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529635243 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635243 Building ZINC001529635933 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529635933 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/492 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c2ccccc2oc1C(=O)c1ccco1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529635933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529635933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001529635933 none O=C(Nc1c2ccccc2oc1C(=O)c1ccco1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 8, 4, 15, 15, 15, 15, 38, 38, 38, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/493 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c2ccccc2oc1C(=O)c1ccco1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529635933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529635933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001529635933 none O=C(Nc1c2ccccc2oc1C(=O)c1ccco1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 8, 4, 15, 15, 15, 15, 38, 38, 38, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529635933 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 Building ZINC001529635933 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529635933 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 492) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c2ccccc2oc1C(=O)c1ccco1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529635933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529635933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001529635933 none O=C(Nc1c2ccccc2oc1C(=O)c1ccco1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 8, 4, 15, 15, 15, 15, 38, 38, 38, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 493) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c2ccccc2oc1C(=O)c1ccco1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529635933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529635933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001529635933 none O=C(Nc1c2ccccc2oc1C(=O)c1ccco1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 8, 4, 15, 15, 15, 15, 38, 38, 38, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529635933 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529635933 Building ZINC001529653846 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529653846 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/494 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)ccc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529653846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529653846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001529653846 none O=C(Nc1cc(Br)ccc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 5, 7, 7, 7, 26, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 3, 7, 7, 7, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/495 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)ccc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529653846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529653846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001529653846 none O=C(Nc1cc(Br)ccc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 3, 7, 7, 7, 26, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 3, 7, 7, 7, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529653846 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 Building ZINC001529653846 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529653846 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 494) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)ccc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529653846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529653846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001529653846 none O=C(Nc1cc(Br)ccc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 5, 7, 7, 7, 26, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 3, 7, 7, 7, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 495) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)ccc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529653846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529653846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001529653846 none O=C(Nc1cc(Br)ccc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 3, 7, 7, 7, 26, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 3, 7, 7, 7, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529653846 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529653846 Building ZINC001529656620 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529656620 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/496 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)sc3c2CCCC3)cc1) `ZINC001529656620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529656620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001529656620 none COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 14, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 18, 11, 18, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 4, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/497 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)sc3c2CCCC3)cc1) `ZINC001529656620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529656620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001529656620 none COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 14, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 16, 10, 16, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 4, 6, 6, 2, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529656620 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 Building ZINC001529656620 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529656620 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 496) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)sc3c2CCCC3)cc1) `ZINC001529656620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529656620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001529656620 none COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 14, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 18, 11, 18, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 4, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 497) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)sc3c2CCCC3)cc1) `ZINC001529656620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529656620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001529656620 none COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 14, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 16, 10, 16, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 4, 6, 6, 2, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529656620 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529656620 Building ZINC001529701196 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529701196 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/498 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529701196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529701196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001529701196 none CC(C)(C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 5, 6, 10, 11, 11, 10, 11, 11, 11, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 10, 18, 18, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 11, 11, 11, 11, 10, 18, 18, 10, 18, 18, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/499 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529701196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529701196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001529701196 none CC(C)(C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 5, 6, 10, 10, 10, 10, 10, 10, 10, 1, 5, 1, 1, 1, 11, 11, 11, 11, 19, 19, 11, 19, 19, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 19, 19, 19, 19, 19, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529701196 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 Building ZINC001529701196 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529701196 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 498) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529701196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529701196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001529701196 none CC(C)(C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 5, 6, 10, 11, 11, 10, 11, 11, 11, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 10, 18, 18, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 11, 11, 11, 11, 10, 18, 18, 10, 18, 18, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 499) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001529701196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529701196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001529701196 none CC(C)(C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 5, 6, 10, 10, 10, 10, 10, 10, 10, 1, 5, 1, 1, 1, 11, 11, 11, 11, 19, 19, 11, 19, 19, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 19, 19, 19, 19, 19, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529701196 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529701196 Building ZINC001529704167 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529704167 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/500 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ccc3c(c2)OCCO3)n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001529704167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529704167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529704167 none O=C(Nc1cccc(c2ccc3c(c2)OCCO3)n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/501 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ccc3c(c2)OCCO3)n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001529704167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529704167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529704167 none O=C(Nc1cccc(c2ccc3c(c2)OCCO3)n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529704167 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 Building ZINC001529704167 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529704167 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 500) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ccc3c(c2)OCCO3)n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001529704167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529704167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529704167 none O=C(Nc1cccc(c2ccc3c(c2)OCCO3)n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 501) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ccc3c(c2)OCCO3)n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001529704167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529704167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001529704167 none O=C(Nc1cccc(c2ccc3c(c2)OCCO3)n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529704167 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529704167 Building ZINC001529743070 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529743070 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/502 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)c1) `ZINC001529743070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529743070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529743070 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 14, 14, 14, 14, 26, 26, 14, 14, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 14, 14, 14, 26, 26, 26, 26, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/503 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)c1) `ZINC001529743070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529743070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529743070 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 13, 13, 13, 13, 25, 25, 16, 19, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 13, 13, 13, 25, 25, 25, 25, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529743070 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 Building ZINC001529743070 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529743070 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 502) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)c1) `ZINC001529743070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529743070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529743070 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 14, 14, 14, 14, 26, 26, 14, 14, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 14, 14, 14, 26, 26, 26, 26, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 503) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)c1) `ZINC001529743070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529743070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001529743070 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 13, 13, 13, 13, 25, 25, 16, 19, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 13, 13, 13, 25, 25, 25, 25, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529743070 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529743070 Building ZINC001529815031 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529815031 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/504 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529815031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529815031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001529815031 none O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 10, 10, 10, 10, 10, 32, 35, 35, 32, 32, 35, 35, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 35, 35, 35, 35, 10, 10, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/505 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529815031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529815031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001529815031 none O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 7, 7, 7, 7, 7, 26, 32, 32, 26, 29, 32, 32, 7, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 32, 32, 32, 32, 7, 7, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529815031 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 Building ZINC001529815031 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529815031 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 504) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529815031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529815031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001529815031 none O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 10, 10, 10, 10, 10, 32, 35, 35, 32, 32, 35, 35, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 35, 35, 35, 35, 10, 10, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 505) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529815031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529815031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001529815031 none O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 7, 7, 7, 7, 7, 26, 32, 32, 26, 29, 32, 32, 7, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 32, 32, 32, 32, 7, 7, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529815031 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815031 Building ZINC001529815032 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529815032 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/506 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529815032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529815032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001529815032 none O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 10, 10, 10, 10, 10, 31, 35, 35, 35, 35, 35, 35, 10, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 35, 35, 35, 35, 10, 10, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/507 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529815032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529815032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001529815032 none O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 10, 10, 10, 10, 10, 30, 34, 34, 33, 34, 34, 34, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 34, 34, 34, 34, 10, 10, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529815032 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 Building ZINC001529815032 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529815032 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 506) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529815032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529815032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001529815032 none O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 10, 10, 10, 10, 10, 31, 35, 35, 35, 35, 35, 35, 10, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 35, 35, 35, 35, 10, 10, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 507) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001529815032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529815032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001529815032 none O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 10, 10, 10, 10, 10, 30, 34, 34, 33, 34, 34, 34, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 34, 34, 34, 34, 10, 10, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529815032 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529815032 Building ZINC001529896398 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529896398 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/508 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cn2)cc1) `ZINC001529896398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529896398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001529896398 none COc1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/509 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cn2)cc1) `ZINC001529896398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529896398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001529896398 none COc1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529896398 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 Building ZINC001529896398 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529896398 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 508) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cn2)cc1) `ZINC001529896398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529896398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001529896398 none COc1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 509) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cn2)cc1) `ZINC001529896398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529896398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001529896398 none COc1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529896398 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529896398 Building ZINC001529897270 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529897270 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/510 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529897270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529897270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001529897270 none O=C(Nc1ccc(OC(F)(F)F)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 29, 35, 35, 35, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/511 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529897270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529897270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001529897270 none O=C(Nc1ccc(OC(F)(F)F)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 30, 35, 35, 35, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529897270 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 Building ZINC001529897270 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529897270 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 510) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529897270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529897270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001529897270 none O=C(Nc1ccc(OC(F)(F)F)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 29, 35, 35, 35, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 511) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001529897270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529897270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001529897270 none O=C(Nc1ccc(OC(F)(F)F)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 30, 35, 35, 35, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529897270 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529897270 Building ZINC001529955333 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529955333 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/512 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)cc(Br)n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001529955333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529955333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001529955333 none O=C(Nc1cc(C(F)(F)F)cc(Br)n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 12, 22, 22, 6, 1, 6] 37 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/513 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)cc(Br)n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001529955333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529955333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001529955333 none O=C(Nc1cc(C(F)(F)F)cc(Br)n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 12, 22, 22, 6, 1, 6] 37 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529955333 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 Building ZINC001529955333 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529955333 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 512) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)cc(Br)n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001529955333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529955333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001529955333 none O=C(Nc1cc(C(F)(F)F)cc(Br)n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 12, 22, 22, 6, 1, 6] 37 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 513) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)cc(Br)n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001529955333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529955333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001529955333 none O=C(Nc1cc(C(F)(F)F)cc(Br)n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 12, 22, 22, 6, 1, 6] 37 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529955333 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529955333 Building ZINC001529998648 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529998648 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/514 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl) `ZINC001529998648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529998648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001529998648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 6, 14, 14, 14, 6, 6, 4, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/515 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl) `ZINC001529998648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529998648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001529998648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529998648 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 Building ZINC001529998648 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529998648 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 514) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl) `ZINC001529998648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529998648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001529998648 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 6, 14, 14, 14, 6, 6, 4, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 515) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl) `ZINC001529998648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529998648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001529998648 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529998648 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998648 Building ZINC001529998649 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529998649 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/516 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl) `ZINC001529998649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529998649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001529998649 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/517 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl) `ZINC001529998649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529998649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001529998649 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 6, 14, 14, 14, 6, 6, 4, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529998649 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 Building ZINC001529998649 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001529998649 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 516) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl) `ZINC001529998649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001529998649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001529998649 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 517) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl) `ZINC001529998649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001529998649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001529998649 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2c[nH]c3cccc(F)c32)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 6, 14, 14, 14, 6, 6, 4, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001529998649 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001529998649 Building ZINC001530011238 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530011238 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/518 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@H](OCC)C12CCCC2) `ZINC001530011238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530011238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011238 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 7, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 7, 11, 14, 14, 14, 14, 22, 22, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 12, 12, 11, 11, 14, 14, 22, 22, 22, 22, 22, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/519 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@H](OCC)C12CCCC2) `ZINC001530011238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530011238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011238 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 8, 14, 17, 17, 17, 17, 28, 30, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 12, 12, 7, 7, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530011238 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 Building ZINC001530011238 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530011238 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 518) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@H](OCC)C12CCCC2) `ZINC001530011238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530011238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011238 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 7, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 7, 11, 14, 14, 14, 14, 22, 22, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 12, 12, 11, 11, 14, 14, 22, 22, 22, 22, 22, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 519) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@H](OCC)C12CCCC2) `ZINC001530011238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530011238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011238 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 8, 14, 17, 17, 17, 17, 28, 30, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 12, 12, 7, 7, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530011238 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011238 Building ZINC001530011239 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530011239 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/520 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@H](OCC)C12CCCC2) `ZINC001530011239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530011239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011239 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 18, 21, 21, 21, 21, 27, 28, 20, 21, 21, 21, 21, 17, 17, 17, 17, 17, 15, 15, 8, 8, 21, 21, 28, 28, 28, 28, 28, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/521 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@H](OCC)C12CCCC2) `ZINC001530011239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530011239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011239 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 8, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 18, 19, 19, 19, 19, 25, 25, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 15, 15, 8, 8, 19, 19, 25, 25, 25, 25, 25, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 120 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530011239 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 Building ZINC001530011239 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530011239 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 520) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@H](OCC)C12CCCC2) `ZINC001530011239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530011239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011239 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 18, 21, 21, 21, 21, 27, 28, 20, 21, 21, 21, 21, 17, 17, 17, 17, 17, 15, 15, 8, 8, 21, 21, 28, 28, 28, 28, 28, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 521) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@H](OCC)C12CCCC2) `ZINC001530011239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530011239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011239 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 8, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 18, 19, 19, 19, 19, 25, 25, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 15, 15, 8, 8, 19, 19, 25, 25, 25, 25, 25, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 120 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530011239 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011239 Building ZINC001530011241 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530011241 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/522 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@@H](OCC)C12CCCC2) `ZINC001530011241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530011241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011241 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 9, 18, 19, 19, 19, 19, 23, 23, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 14, 14, 10, 10, 19, 19, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/523 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@@H](OCC)C12CCCC2) `ZINC001530011241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530011241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011241 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 10, 18, 20, 20, 20, 20, 25, 25, 20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 14, 14, 7, 7, 20, 20, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530011241 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 Building ZINC001530011241 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530011241 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 522) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@@H](OCC)C12CCCC2) `ZINC001530011241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530011241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011241 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 9, 18, 19, 19, 19, 19, 23, 23, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 14, 14, 10, 10, 19, 19, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 523) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@@H](OCC)C12CCCC2) `ZINC001530011241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530011241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011241 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1C[C@@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 10, 18, 20, 20, 20, 20, 25, 25, 20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 14, 14, 7, 7, 20, 20, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530011241 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011241 Building ZINC001530011244 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530011244 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/524 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@@H](OCC)C12CCCC2) `ZINC001530011244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530011244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011244 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 8, 13, 16, 16, 16, 16, 27, 29, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 7, 7, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/525 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@@H](OCC)C12CCCC2) `ZINC001530011244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530011244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011244 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 8, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 8, 12, 16, 16, 16, 16, 24, 24, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 13, 13, 10, 10, 16, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530011244 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 Building ZINC001530011244 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530011244 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 524) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@@H](OCC)C12CCCC2) `ZINC001530011244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530011244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011244 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 8, 13, 16, 16, 16, 16, 27, 29, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 7, 7, 16, 16, 29, 29, 29, 29, 29, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 525) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@@H](OCC)C12CCCC2) `ZINC001530011244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530011244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001530011244 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1C[C@@H](OCC)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 8, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 8, 12, 16, 16, 16, 16, 24, 24, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 13, 13, 10, 10, 16, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530011244 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530011244 Building ZINC001530035358 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530035358 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/526 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(Br)ccc(Cl)c2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001530035358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530035358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001530035358 none O=C(Nc1ccc2c(Br)ccc(Cl)c2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/527 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(Br)ccc(Cl)c2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001530035358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530035358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001530035358 none O=C(Nc1ccc2c(Br)ccc(Cl)c2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530035358 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 Building ZINC001530035358 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530035358 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 526) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(Br)ccc(Cl)c2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001530035358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530035358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001530035358 none O=C(Nc1ccc2c(Br)ccc(Cl)c2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 527) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(Br)ccc(Cl)c2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001530035358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530035358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001530035358 none O=C(Nc1ccc2c(Br)ccc(Cl)c2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530035358 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530035358 Building ZINC001530042277 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530042277 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/528 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(C)cc1) `ZINC001530042277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530042277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001530042277 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/529 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(C)cc1) `ZINC001530042277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530042277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001530042277 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530042277 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 Building ZINC001530042277 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530042277 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 528) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(C)cc1) `ZINC001530042277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530042277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001530042277 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 529) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(C)cc1) `ZINC001530042277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530042277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001530042277 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530042277 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042277 Building ZINC001530042278 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530042278 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/530 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(C)cc1) `ZINC001530042278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530042278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001530042278 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/531 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(C)cc1) `ZINC001530042278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530042278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001530042278 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530042278 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 Building ZINC001530042278 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530042278 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 530) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(C)cc1) `ZINC001530042278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530042278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001530042278 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 531) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(C)cc1) `ZINC001530042278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530042278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001530042278 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530042278 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530042278 Building ZINC001530051096 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530051096 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/532 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cncc(F)c2)ccc1C) `ZINC001530051096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530051096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001530051096 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cncc(F)c2)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 15, 1, 1, 1, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 8, 30, 30, 30, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 55 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/533 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cncc(F)c2)ccc1C) `ZINC001530051096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530051096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001530051096 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cncc(F)c2)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 15, 1, 1, 1, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 8, 27, 27, 27, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530051096 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 Building ZINC001530051096 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530051096 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 532) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cncc(F)c2)ccc1C) `ZINC001530051096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530051096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001530051096 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cncc(F)c2)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 15, 1, 1, 1, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 8, 30, 30, 30, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 55 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 533) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cncc(F)c2)ccc1C) `ZINC001530051096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530051096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001530051096 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cncc(F)c2)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 15, 1, 1, 1, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 8, 27, 27, 27, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530051096 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530051096 Building ZINC001530197551 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530197551 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/534 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001530197551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530197551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001530197551 none COc1ccc(Cl)cc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 14, 14, 6, 14, 14, 14, 6, 4, 6, 6, 11, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 19, 19, 19, 14, 10, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 10, 12, 12, 12, 12, 12, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/535 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001530197551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530197551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001530197551 none COc1ccc(Cl)cc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 12, 16, 16, 16, 8, 5, 8, 8, 12, 12, 12, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 11, 11, 7, 11, 11, 7, 19, 19, 19, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 7, 11, 11, 7, 11, 11, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530197551 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 Building ZINC001530197551 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530197551 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 534) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001530197551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530197551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001530197551 none COc1ccc(Cl)cc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 14, 14, 6, 14, 14, 14, 6, 4, 6, 6, 11, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 19, 19, 19, 14, 10, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 10, 12, 12, 12, 12, 12, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 535) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001530197551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530197551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001530197551 none COc1ccc(Cl)cc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 12, 16, 16, 16, 8, 5, 8, 8, 12, 12, 12, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 11, 11, 7, 11, 11, 7, 19, 19, 19, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 7, 11, 11, 7, 11, 11, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530197551 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197551 Building ZINC001530197554 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530197554 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/536 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001530197554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530197554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001530197554 none COc1ccc(Cl)cc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 9, 16, 16, 16, 8, 5, 8, 8, 9, 9, 9, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 14, 14, 11, 14, 14, 11, 21, 21, 21, 16, 14, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 11, 14, 14, 11, 14, 14, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/537 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001530197554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530197554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001530197554 none COc1ccc(Cl)cc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 18, 18, 10, 18, 18, 18, 7, 5, 7, 7, 9, 9, 9, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 20, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530197554 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 Building ZINC001530197554 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530197554 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 536) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001530197554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530197554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001530197554 none COc1ccc(Cl)cc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 9, 16, 16, 16, 8, 5, 8, 8, 9, 9, 9, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 14, 14, 11, 14, 14, 11, 21, 21, 21, 16, 14, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 11, 14, 14, 11, 14, 14, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 537) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001530197554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530197554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001530197554 none COc1ccc(Cl)cc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 18, 18, 10, 18, 18, 18, 7, 5, 7, 7, 9, 9, 9, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 20, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530197554 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530197554 Building ZINC001530221734 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530221734 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/538 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1) `ZINC001530221734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530221734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001530221734 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 29, 29, 29, 29, 43, 43, 43, 43, 43, 43, 43, 43, 29, 29, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 43, 43, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/539 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1) `ZINC001530221734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530221734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001530221734 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 15, 27, 27, 27, 27, 44, 44, 44, 40, 42, 44, 44, 44, 27, 27, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 44, 44, 27, 27, 27, 27] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530221734 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 Building ZINC001530221734 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530221734 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 538) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1) `ZINC001530221734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530221734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001530221734 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 29, 29, 29, 29, 43, 43, 43, 43, 43, 43, 43, 43, 29, 29, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 43, 43, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 539) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1) `ZINC001530221734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530221734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001530221734 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 15, 27, 27, 27, 27, 44, 44, 44, 40, 42, 44, 44, 44, 27, 27, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 44, 44, 27, 27, 27, 27] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530221734 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530221734 Building ZINC001530236243 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530236243 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/540 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)cc1) `ZINC001530236243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530236243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001530236243 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 2, 9, 9, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 13, 13, 11, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 13, 13, 13, 13, 2, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/541 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)cc1) `ZINC001530236243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530236243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001530236243 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 2, 11, 11, 12, 12, 12, 12, 24, 24, 49, 49, 49, 49, 12, 12, 12, 12, 14, 14, 12, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49, 12, 12, 14, 14, 14, 14, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530236243 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 Building ZINC001530236243 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530236243 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 540) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)cc1) `ZINC001530236243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530236243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001530236243 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 2, 9, 9, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 11, 11, 11, 11, 13, 13, 11, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 13, 13, 13, 13, 2, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 541) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)cc1) `ZINC001530236243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530236243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001530236243 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 2, 11, 11, 12, 12, 12, 12, 24, 24, 49, 49, 49, 49, 12, 12, 12, 12, 14, 14, 12, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49, 12, 12, 14, 14, 14, 14, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530236243 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236243 Building ZINC001530236245 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530236245 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/542 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)cc1) `ZINC001530236245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530236245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001530236245 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 2, 9, 10, 11, 11, 11, 11, 25, 25, 49, 49, 49, 49, 11, 11, 11, 11, 13, 13, 12, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 49, 49, 49, 49, 49, 49, 49, 49, 49, 11, 11, 13, 13, 12, 13, 2, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/543 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)cc1) `ZINC001530236245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530236245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001530236245 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 2, 7, 8, 10, 10, 10, 10, 25, 25, 49, 50, 50, 50, 10, 10, 10, 10, 12, 12, 10, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 12, 12, 10, 12, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530236245 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 Building ZINC001530236245 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530236245 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 542) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)cc1) `ZINC001530236245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530236245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001530236245 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 2, 9, 10, 11, 11, 11, 11, 25, 25, 49, 49, 49, 49, 11, 11, 11, 11, 13, 13, 12, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 49, 49, 49, 49, 49, 49, 49, 49, 49, 11, 11, 13, 13, 12, 13, 2, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 543) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)cc1) `ZINC001530236245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530236245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001530236245 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 2, 7, 8, 10, 10, 10, 10, 25, 25, 49, 50, 50, 50, 10, 10, 10, 10, 12, 12, 10, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 12, 12, 10, 12, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530236245 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530236245 Building ZINC001530243388 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530243388 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/544 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1c1ccccc1) `ZINC001530243388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530243388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530243388 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1c1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/545 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1c1ccccc1) `ZINC001530243388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530243388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530243388 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1c1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530243388 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 Building ZINC001530243388 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530243388 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 544) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1c1ccccc1) `ZINC001530243388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530243388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530243388 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1c1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 545) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1c1ccccc1) `ZINC001530243388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530243388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530243388 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1c1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530243388 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530243388 Building ZINC001530298757 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530298757 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/546 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1Br) `ZINC001530298757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530298757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001530298757 none CSc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 14, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 34, 34, 34, 14, 14, 4, 9, 9, 14] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/547 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1Br) `ZINC001530298757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530298757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001530298757 none CSc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 11, 14, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 34, 34, 34, 14, 14, 4, 9, 9, 14] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530298757 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 Building ZINC001530298757 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530298757 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 546) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1Br) `ZINC001530298757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530298757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001530298757 none CSc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 14, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 34, 34, 34, 14, 14, 4, 9, 9, 14] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 547) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1Br) `ZINC001530298757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530298757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001530298757 none CSc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 11, 14, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 34, 34, 34, 14, 14, 4, 9, 9, 14] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530298757 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530298757 Building ZINC001530321244 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530321244 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/548 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001530321244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530321244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001530321244 none O=C(N1CCN(c2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 9, 14, 14, 14, 14, 47, 47, 40, 47, 47, 47, 47, 47, 47, 14, 14, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 47, 47, 42, 47, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/549 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001530321244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530321244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001530321244 none O=C(N1CCN(c2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 14, 14, 14, 14, 47, 47, 39, 47, 47, 47, 47, 47, 47, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 47, 47, 42, 47, 14, 14, 14, 14, 3, 1, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530321244 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 Building ZINC001530321244 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530321244 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 548) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001530321244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530321244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001530321244 none O=C(N1CCN(c2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 9, 14, 14, 14, 14, 47, 47, 40, 47, 47, 47, 47, 47, 47, 14, 14, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 47, 47, 42, 47, 14, 14, 14, 14, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 549) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001530321244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530321244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001530321244 none O=C(N1CCN(c2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 14, 14, 14, 14, 47, 47, 39, 47, 47, 47, 47, 47, 47, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 47, 47, 42, 47, 14, 14, 14, 14, 3, 1, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530321244 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530321244 Building ZINC001530330896 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530330896 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/550 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nsc2ccccc21) `ZINC001530330896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530330896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001530330896 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nsc2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 2, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/551 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nsc2ccccc21) `ZINC001530330896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530330896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001530330896 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nsc2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 21, 21, 7, 21, 4, 4, 4, 2, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530330896 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 Building ZINC001530330896 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530330896 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 550) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nsc2ccccc21) `ZINC001530330896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530330896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001530330896 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nsc2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 2, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 551) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nsc2ccccc21) `ZINC001530330896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530330896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001530330896 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nsc2ccccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 21, 21, 7, 21, 4, 4, 4, 2, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530330896 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530330896 Building ZINC001530386188 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530386188 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/552 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(Br)cc3)CC2)cc1Cl) `ZINC001530386188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530386188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001530386188 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(Br)cc3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 5, 10, 14, 14, 14, 14, 21, 21, 21, 21, 21, 21, 14, 14, 6, 6, 6, 14, 14, 14, 6, 6, 14, 14, 14, 14, 14, 21, 21, 21, 21, 14, 14, 14, 14, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/553 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(Br)cc3)CC2)cc1Cl) `ZINC001530386188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530386188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001530386188 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(Br)cc3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 22, 22, 18, 22, 22, 22, 14, 14, 6, 6, 6, 14, 14, 14, 6, 6, 14, 14, 14, 14, 14, 22, 22, 22, 22, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530386188 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 Building ZINC001530386188 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530386188 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 552) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(Br)cc3)CC2)cc1Cl) `ZINC001530386188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530386188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001530386188 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(Br)cc3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 5, 10, 14, 14, 14, 14, 21, 21, 21, 21, 21, 21, 14, 14, 6, 6, 6, 14, 14, 14, 6, 6, 14, 14, 14, 14, 14, 21, 21, 21, 21, 14, 14, 14, 14, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 553) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(Br)cc3)CC2)cc1Cl) `ZINC001530386188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530386188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001530386188 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(Br)cc3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 22, 22, 18, 22, 22, 22, 14, 14, 6, 6, 6, 14, 14, 14, 6, 6, 14, 14, 14, 14, 14, 22, 22, 22, 22, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530386188 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530386188 Building ZINC001530412371 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530412371 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/554 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc2ccc(Cl)cc2C(F)(F)F)C(C)C)c1) `ZINC001530412371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530412371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001530412371 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc2ccc(Cl)cc2C(F)(F)F)C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 12, 17, 17, 17, 23, 23, 19, 22, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 12, 12, 17, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/555 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(CC(=O)Nc2ccc(Cl)cc2C(F)(F)F)C(C)C)c1) `ZINC001530412371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530412371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001530412371 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(CC(=O)Nc2ccc(Cl)cc2C(F)(F)F)C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 12, 16, 16, 16, 23, 23, 16, 16, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 12, 12, 16, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530412371 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 Building ZINC001530412371 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530412371 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 554) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc2ccc(Cl)cc2C(F)(F)F)C(C)C)c1) `ZINC001530412371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530412371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001530412371 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(CC(=O)Nc2ccc(Cl)cc2C(F)(F)F)C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 12, 17, 17, 17, 23, 23, 19, 22, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 12, 12, 17, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 555) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(CC(=O)Nc2ccc(Cl)cc2C(F)(F)F)C(C)C)c1) `ZINC001530412371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530412371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001530412371 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(CC(=O)Nc2ccc(Cl)cc2C(F)(F)F)C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 12, 16, 16, 16, 23, 23, 16, 16, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 12, 12, 16, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530412371 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530412371 Building ZINC001530427390 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530427390 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/556 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530427390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530427390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530427390 none O=C(Nc1cccc(OCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 24, 30, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 30, 30, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/557 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530427390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530427390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530427390 none O=C(Nc1cccc(OCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 24, 30, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 30, 30, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530427390 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 Building ZINC001530427390 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530427390 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 556) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530427390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530427390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530427390 none O=C(Nc1cccc(OCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 24, 30, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 30, 30, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 557) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530427390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530427390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530427390 none O=C(Nc1cccc(OCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 24, 30, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 30, 30, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530427390 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530427390 Building ZINC001530585695 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530585695 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/558 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(F)c2)cc1Cl) `ZINC001530585695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530585695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530585695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/559 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(F)c2)cc1Cl) `ZINC001530585695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530585695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530585695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 9, 9, 9, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530585695 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 Building ZINC001530585695 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530585695 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 558) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(F)c2)cc1Cl) `ZINC001530585695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530585695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530585695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 559) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(F)c2)cc1Cl) `ZINC001530585695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530585695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530585695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 9, 9, 9, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530585695 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585695 Building ZINC001530585696 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530585696 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/560 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(F)c2)cc1Cl) `ZINC001530585696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530585696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530585696 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 9, 9, 9, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/561 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(F)c2)cc1Cl) `ZINC001530585696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530585696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530585696 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 7, 7, 7, 4, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530585696 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 Building ZINC001530585696 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530585696 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 560) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(F)c2)cc1Cl) `ZINC001530585696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530585696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530585696 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 9, 9, 9, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 561) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(F)c2)cc1Cl) `ZINC001530585696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530585696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530585696 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 7, 7, 7, 4, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530585696 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530585696 Building ZINC001530630765 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530630765 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/562 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ncc3n2CCCC3)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530630765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530630765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530630765 none O=C(Nc1cccc(c2ncc3n2CCCC3)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 36, 36, 36, 36, 36, 15, 1, 1, 1, 8, 8, 8, 8, 8, 4, 15, 15, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/563 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ncc3n2CCCC3)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530630765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530630765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530630765 none O=C(Nc1cccc(c2ncc3n2CCCC3)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 18, 18, 18, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 18, 1, 1, 1, 8, 8, 8, 8, 8, 4, 18, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530630765 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 Building ZINC001530630765 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530630765 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 562) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ncc3n2CCCC3)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530630765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530630765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530630765 none O=C(Nc1cccc(c2ncc3n2CCCC3)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 36, 36, 36, 36, 36, 15, 1, 1, 1, 8, 8, 8, 8, 8, 4, 15, 15, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 563) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ncc3n2CCCC3)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530630765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530630765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530630765 none O=C(Nc1cccc(c2ncc3n2CCCC3)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 18, 18, 18, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 18, 1, 1, 1, 8, 8, 8, 8, 8, 4, 18, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530630765 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530630765 Building ZINC001530631294 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530631294 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/564 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001530631294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530631294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001530631294 none O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 3, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/565 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001530631294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530631294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001530631294 none O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 3, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530631294 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 Building ZINC001530631294 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530631294 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 564) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001530631294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530631294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001530631294 none O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 3, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 565) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001530631294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530631294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001530631294 none O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 3, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530631294 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631294 Building ZINC001530631426 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530631426 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/566 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001530631426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530631426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530631426 none O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 7, 7, 20, 50, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/567 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001530631426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530631426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530631426 none O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 7, 7, 19, 50, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530631426 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 Building ZINC001530631426 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530631426 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 566) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001530631426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530631426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530631426 none O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 7, 7, 20, 50, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 567) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001530631426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530631426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001530631426 none O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 7, 7, 19, 50, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530631426 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530631426 Building ZINC001530632947 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530632947 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/568 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530632947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632947 none CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 3, 8, 8, 2, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 8, 8, 8, 2, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/569 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530632947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632947 none CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 10, 2, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530632947 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 Building ZINC001530632947 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530632947 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 568) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530632947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632947 none CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 3, 8, 8, 2, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 8, 8, 8, 2, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 569) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530632947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632947 none CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 10, 2, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530632947 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632947 Building ZINC001530632948 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530632948 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/570 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530632948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632948 none CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 11, 2, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/571 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530632948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632948 none CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 9, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 4, 17, 17, 8, 17, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 91 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530632948 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 Building ZINC001530632948 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530632948 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 570) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530632948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632948 none CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 11, 2, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 571) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530632948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632948 none CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 9, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 4, 17, 17, 8, 17, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 91 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530632948 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632948 Building ZINC001530632949 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530632949 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/572 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530632949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632949 none CC[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 9, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 4, 16, 16, 4, 16, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/573 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530632949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632949 none CC[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 9, 9, 2, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 5, 17, 17, 17, 17, 17, 17, 3, 3, 4, 4, 4, 4, 11, 11, 11, 11, 11, 9, 9, 9, 2, 3, 3, 3, 17, 17, 6, 17, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530632949 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 Building ZINC001530632949 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530632949 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 572) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530632949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632949 none CC[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 9, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 4, 16, 16, 4, 16, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 573) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530632949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632949 none CC[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 9, 9, 2, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 5, 17, 17, 17, 17, 17, 17, 3, 3, 4, 4, 4, 4, 11, 11, 11, 11, 11, 9, 9, 9, 2, 3, 3, 3, 17, 17, 6, 17, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530632949 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632949 Building ZINC001530632950 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530632950 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/574 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530632950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632950 none CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 10, 10, 2, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 4, 4, 4, 4, 13, 13, 13, 13, 13, 10, 10, 10, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/575 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530632950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632950 none CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 4, 10, 10, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 10, 10, 10, 2, 4, 4, 4, 18, 18, 4, 18, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 94 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530632950 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 Building ZINC001530632950 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530632950 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 574) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530632950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632950 none CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 10, 10, 2, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 4, 4, 4, 4, 13, 13, 13, 13, 13, 10, 10, 10, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 575) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001530632950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530632950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001530632950 none CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 4, 10, 10, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 10, 10, 10, 2, 4, 4, 4, 18, 18, 4, 18, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 94 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530632950 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530632950 Building ZINC001530639738 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530639738 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/576 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001530639738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530639738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001530639738 none O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 33, 33, 33, 33, 50, 50, 50, 49, 50, 50, 50, 50, 33, 33, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 50, 50, 33, 33, 33, 33, 3, 3, 3, 3] 50 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/577 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001530639738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530639738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001530639738 none O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 18, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530639738 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 Building ZINC001530639738 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530639738 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 576) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001530639738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530639738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001530639738 none O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 33, 33, 33, 33, 50, 50, 50, 49, 50, 50, 50, 50, 33, 33, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 50, 50, 33, 33, 33, 33, 3, 3, 3, 3] 50 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 577) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001530639738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530639738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001530639738 none O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 18, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530639738 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530639738 Building ZINC001530699018 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001530699018 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/578 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 20, 23, 23, 21, 23, 23, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 23, 23, 23, 23, 23, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/579 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 14, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/580 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/580' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 20, 23, 23, 21, 23, 23, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 23, 23, 23, 23, 23, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/581 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/581' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 14, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530699018 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 Building ZINC001530699018 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001530699018 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 578) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 20, 23, 23, 21, 23, 23, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 23, 23, 23, 23, 23, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 579) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 14, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 580) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 20, 23, 23, 21, 23, 23, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 23, 23, 23, 23, 23, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 581) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 14, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530699018 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 Building ZINC001530699018 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001530699018 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 578) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 20, 23, 23, 21, 23, 23, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 23, 23, 23, 23, 23, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 579) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 14, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 580) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 20, 23, 23, 21, 23, 23, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 23, 23, 23, 23, 23, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 581) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 14, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530699018 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 Building ZINC001530699018 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001530699018 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 578) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 20, 23, 23, 21, 23, 23, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 23, 23, 23, 23, 23, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 579) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 14, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 580) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 20, 23, 23, 21, 23, 23, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 23, 23, 23, 23, 23, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 581) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl) `ZINC001530699018.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001530699018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001530699018 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3ccccc3)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 14, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530699018 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530699018 Building ZINC001530803856 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530803856 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/582 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/582' -> `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(c1cc(C)ccc1C)C1CCOCC1) `ZINC001530803856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530803856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001530803856 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(c1cc(C)ccc1C)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 4, 4, 10, 15, 15, 15, 10, 15, 15, 15, 10, 15, 15, 15, 15, 15, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 15, 15, 15, 15, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 38 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 94 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/583 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/583' -> `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(c1cc(C)ccc1C)C1CCOCC1) `ZINC001530803856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530803856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001530803856 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(c1cc(C)ccc1C)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 4, 4, 11, 16, 16, 16, 11, 16, 16, 16, 11, 17, 17, 17, 17, 17, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 16, 16, 16, 16, 11, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17] 39 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 96 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530803856 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 Building ZINC001530803856 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530803856 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 582) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1cc(C)ccc1C)C1CCOCC1) `ZINC001530803856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530803856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001530803856 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(c1cc(C)ccc1C)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 4, 4, 10, 15, 15, 15, 10, 15, 15, 15, 10, 15, 15, 15, 15, 15, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 15, 15, 15, 15, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 38 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 94 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 583) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1cc(C)ccc1C)C1CCOCC1) `ZINC001530803856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530803856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001530803856 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(c1cc(C)ccc1C)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 4, 4, 11, 16, 16, 16, 11, 16, 16, 16, 11, 17, 17, 17, 17, 17, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 16, 16, 16, 16, 11, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17] 39 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 96 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530803856 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530803856 Building ZINC001530824853 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530824853 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/584 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1) `ZINC001530824853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530824853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001530824853 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 6, 6, 11, 18, 18, 16, 18, 18, 18, 18, 6, 9, 9, 6, 6, 9, 9, 8, 8, 18, 18, 18, 18, 18, 8, 4, 11, 11, 18, 18, 18, 9, 9, 9, 9, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/585 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1) `ZINC001530824853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530824853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001530824853 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 18, 18, 16, 16, 18, 18, 18, 6, 10, 10, 6, 6, 10, 10, 7, 7, 15, 15, 15, 15, 15, 7, 4, 12, 12, 18, 18, 18, 10, 10, 10, 10, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530824853 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 Building ZINC001530824853 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530824853 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 584) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1) `ZINC001530824853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530824853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001530824853 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 6, 6, 11, 18, 18, 16, 18, 18, 18, 18, 6, 9, 9, 6, 6, 9, 9, 8, 8, 18, 18, 18, 18, 18, 8, 4, 11, 11, 18, 18, 18, 9, 9, 9, 9, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 585) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1) `ZINC001530824853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530824853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001530824853 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 18, 18, 16, 16, 18, 18, 18, 6, 10, 10, 6, 6, 10, 10, 7, 7, 15, 15, 15, 15, 15, 7, 4, 12, 12, 18, 18, 18, 10, 10, 10, 10, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530824853 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824853 Building ZINC001530824854 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530824854 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/586 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1) `ZINC001530824854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530824854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001530824854 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 18, 18, 16, 17, 18, 18, 18, 6, 10, 10, 6, 6, 10, 10, 7, 7, 14, 14, 14, 14, 14, 7, 4, 12, 12, 18, 18, 18, 10, 10, 10, 10, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/587 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1) `ZINC001530824854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530824854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001530824854 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 19, 19, 17, 17, 19, 19, 19, 6, 9, 9, 8, 7, 9, 9, 8, 8, 17, 17, 17, 17, 17, 8, 4, 12, 12, 19, 19, 19, 9, 9, 9, 9, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530824854 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 Building ZINC001530824854 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530824854 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 586) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1) `ZINC001530824854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530824854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001530824854 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 18, 18, 16, 17, 18, 18, 18, 6, 10, 10, 6, 6, 10, 10, 7, 7, 14, 14, 14, 14, 14, 7, 4, 12, 12, 18, 18, 18, 10, 10, 10, 10, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 587) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1) `ZINC001530824854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530824854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001530824854 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2Cl)c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 6, 6, 12, 19, 19, 17, 17, 19, 19, 19, 6, 9, 9, 8, 7, 9, 9, 8, 8, 17, 17, 17, 17, 17, 8, 4, 12, 12, 19, 19, 19, 9, 9, 9, 9, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530824854 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530824854 Building ZINC001530828217 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530828217 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/588 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(C(C)(C)C)co1) `ZINC001530828217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530828217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001530828217 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(C(C)(C)C)co1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 4, 28, 28, 28, 28, 28, 28, 4, 4, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 9, 9, 9, 5, 5, 4, 4, 4, 28, 28, 6, 28, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/589 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(C(C)(C)C)co1) `ZINC001530828217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530828217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001530828217 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(C(C)(C)C)co1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530828217 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 Building ZINC001530828217 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530828217 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 588) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(C(C)(C)C)co1) `ZINC001530828217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530828217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001530828217 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(C(C)(C)C)co1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 4, 28, 28, 28, 28, 28, 28, 4, 4, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 9, 9, 9, 5, 5, 4, 4, 4, 28, 28, 6, 28, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 589) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(C(C)(C)C)co1) `ZINC001530828217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530828217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001530828217 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(C(C)(C)C)co1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530828217 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530828217 Building ZINC001530834472 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530834472 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/590 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1) `ZINC001530834472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530834472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001530834472 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 32, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 32, 49, 49, 32, 32, 50, 50, 49, 49, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 50, 49, 49, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/591 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1) `ZINC001530834472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530834472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001530834472 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 29, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 43, 43, 29, 29, 45, 45, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 49, 49, 49, 49, 49, 43, 43, 45, 45, 45, 45, 45, 45, 43, 43, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530834472 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 Building ZINC001530834472 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530834472 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 590) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1) `ZINC001530834472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530834472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001530834472 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 32, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 32, 49, 49, 32, 32, 50, 50, 49, 49, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 50, 49, 49, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 591) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1) `ZINC001530834472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530834472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001530834472 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 29, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 43, 43, 29, 29, 45, 45, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 49, 49, 49, 49, 49, 43, 43, 45, 45, 45, 45, 45, 45, 43, 43, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530834472 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834472 Building ZINC001530834473 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530834473 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/592 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1) `ZINC001530834473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530834473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001530834473 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 29, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 42, 42, 29, 29, 44, 44, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 49, 49, 49, 49, 49, 42, 42, 44, 44, 44, 44, 44, 44, 42, 42, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/593 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1) `ZINC001530834473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530834473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001530834473 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 32, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 32, 47, 47, 32, 32, 49, 49, 47, 47, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 49, 49, 49, 49, 49, 47, 47, 49, 49, 49, 49, 49, 49, 47, 47, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530834473 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 Building ZINC001530834473 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530834473 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 592) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1) `ZINC001530834473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530834473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001530834473 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 29, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 42, 42, 29, 29, 44, 44, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 49, 49, 49, 49, 49, 42, 42, 44, 44, 44, 44, 44, 44, 42, 42, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 593) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1) `ZINC001530834473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530834473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001530834473 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccc(N(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 32, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 32, 47, 47, 32, 32, 49, 49, 47, 47, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 49, 49, 49, 49, 49, 47, 47, 49, 49, 49, 49, 49, 49, 47, 47, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530834473 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530834473 Building ZINC001530920852 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530920852 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/594 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCc1ccc(Cl)cc1)CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530920852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530920852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001530920852 none O=C(N(CCc1ccc(Cl)cc1)CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 13, 13, 17, 17, 13, 13, 17, 17, 6, 14, 24, 24, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 14, 14, 24, 24, 24, 24, 24, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/595 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCc1ccc(Cl)cc1)CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530920852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530920852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001530920852 none O=C(N(CCc1ccc(Cl)cc1)CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 10, 10, 14, 14, 10, 11, 14, 14, 5, 15, 31, 31, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 14, 14, 14, 14, 15, 15, 31, 31, 31, 31, 31, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530920852 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 Building ZINC001530920852 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001530920852 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 594) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCc1ccc(Cl)cc1)CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530920852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001530920852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001530920852 none O=C(N(CCc1ccc(Cl)cc1)CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 13, 13, 17, 17, 13, 13, 17, 17, 6, 14, 24, 24, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 14, 14, 24, 24, 24, 24, 24, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 595) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCc1ccc(Cl)cc1)CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001530920852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001530920852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001530920852 none O=C(N(CCc1ccc(Cl)cc1)CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 10, 10, 14, 14, 10, 11, 14, 14, 5, 15, 31, 31, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 14, 14, 14, 14, 15, 15, 31, 31, 31, 31, 31, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001530920852 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001530920852 Building ZINC001531036439 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531036439 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/596 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1I) `ZINC001531036439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531036439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001531036439 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 18, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 7, 7, 1, 7, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 7, 6, 1, 6, 34] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/597 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1I) `ZINC001531036439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531036439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001531036439 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 18, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 7, 7, 1, 7, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 7, 6, 1, 6, 31] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531036439 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 Building ZINC001531036439 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531036439 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 596) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1I) `ZINC001531036439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531036439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001531036439 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 18, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 7, 7, 1, 7, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 7, 6, 1, 6, 34] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 597) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1I) `ZINC001531036439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531036439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001531036439 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 18, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 7, 7, 1, 7, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 7, 6, 1, 6, 31] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531036439 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531036439 Building ZINC001531048549 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531048549 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/598 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(F)(F)F)c1)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC001531048549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531048549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001531048549 none O=C(Nc1cccc(C(F)(F)F)c1)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 50, 50, 25, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 18, 50, 50, 38, 50, 12, 12, 12, 3, 2, 2, 2, 2, 12] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/599 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(F)(F)F)c1)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC001531048549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531048549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001531048549 none O=C(Nc1cccc(C(F)(F)F)c1)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 17, 50, 50, 17, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 17, 50, 50, 29, 50, 11, 11, 11, 3, 2, 2, 2, 2, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531048549 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 Building ZINC001531048549 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531048549 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 598) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(F)(F)F)c1)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC001531048549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531048549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001531048549 none O=C(Nc1cccc(C(F)(F)F)c1)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 50, 50, 25, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 18, 50, 50, 38, 50, 12, 12, 12, 3, 2, 2, 2, 2, 12] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 599) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(F)(F)F)c1)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC001531048549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531048549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001531048549 none O=C(Nc1cccc(C(F)(F)F)c1)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 17, 50, 50, 17, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 17, 50, 50, 29, 50, 11, 11, 11, 3, 2, 2, 2, 2, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531048549 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531048549 Building ZINC001531086882 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531086882 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/600 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/600' -> `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)Nc1sccc1C(=O)c1ccc(C)cc1) `ZINC001531086882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531086882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531086882 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1sccc1C(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 22, 22, 32, 32, 32, 32, 32, 32, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 8, 8, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/601 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/601' -> `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)Nc1sccc1C(=O)c1ccc(C)cc1) `ZINC001531086882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531086882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531086882 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1sccc1C(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 22, 22, 35, 35, 27, 27, 35, 35, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 9, 9, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531086882 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 Building ZINC001531086882 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531086882 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 600) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1sccc1C(=O)c1ccc(C)cc1) `ZINC001531086882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531086882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531086882 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1sccc1C(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 22, 22, 32, 32, 32, 32, 32, 32, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 8, 8, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 601) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1sccc1C(=O)c1ccc(C)cc1) `ZINC001531086882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531086882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531086882 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1sccc1C(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 22, 22, 35, 35, 27, 27, 35, 35, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 9, 9, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531086882 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531086882 Building ZINC001531098913 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531098913 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/602 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc2nc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)sc2c1C) `ZINC001531098913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531098913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001531098913 none CCOC(=O)c1sc2nc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)sc2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 39, 35, 8, 35, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 44, 44, 44, 44, 44, 4, 3, 1, 3, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/603 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc2nc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)sc2c1C) `ZINC001531098913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531098913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001531098913 none CCOC(=O)c1sc2nc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)sc2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 39, 35, 8, 35, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 44, 44, 44, 44, 44, 4, 3, 1, 3, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531098913 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 Building ZINC001531098913 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531098913 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 602) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc2nc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)sc2c1C) `ZINC001531098913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531098913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001531098913 none CCOC(=O)c1sc2nc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)sc2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 39, 35, 8, 35, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 44, 44, 44, 44, 44, 4, 3, 1, 3, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 603) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc2nc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)sc2c1C) `ZINC001531098913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531098913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001531098913 none CCOC(=O)c1sc2nc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)sc2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 39, 35, 8, 35, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 44, 44, 44, 44, 44, 4, 3, 1, 3, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531098913 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531098913 Building ZINC001531120266 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531120266 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/604 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2c1cc(Br)cc2C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001531120266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531120266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531120266 none O=C(N1CCOc2c1cc(Br)cc2C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 19 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/605 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2c1cc(Br)cc2C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001531120266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531120266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531120266 none O=C(N1CCOc2c1cc(Br)cc2C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 1, 1, 5, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5] 20 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531120266 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 Building ZINC001531120266 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531120266 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 604) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2c1cc(Br)cc2C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001531120266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531120266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531120266 none O=C(N1CCOc2c1cc(Br)cc2C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 19 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 605) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2c1cc(Br)cc2C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001531120266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531120266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531120266 none O=C(N1CCOc2c1cc(Br)cc2C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 1, 1, 5, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5] 20 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531120266 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531120266 Building ZINC001531167386 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531167386 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/606 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)cc(Cl)c1) `ZINC001531167386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531167386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001531167386 none COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 6, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 8, 8, 8, 3, 8, 8, 8, 21, 21, 21, 12, 12, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 3, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/607 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)cc(Cl)c1) `ZINC001531167386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531167386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001531167386 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 6, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 8, 8, 8, 3, 8, 8, 8, 21, 21, 21, 12, 12, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 3, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531167386 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 Building ZINC001531167386 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531167386 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 606) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)cc(Cl)c1) `ZINC001531167386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531167386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001531167386 none COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 6, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 8, 8, 8, 3, 8, 8, 8, 21, 21, 21, 12, 12, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 3, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 607) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)cc(Cl)c1) `ZINC001531167386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531167386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001531167386 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 6, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 8, 8, 8, 3, 8, 8, 8, 21, 21, 21, 12, 12, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 3, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531167386 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531167386 Building ZINC001531334054 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531334054 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/608 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 16, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/609 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 16, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/610 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/610' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 17, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/611 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/611' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 17, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531334054 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 Building ZINC001531334054 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531334054 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 608) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 16, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 609) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 16, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 610) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 17, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 611) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 17, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531334054 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 Building ZINC001531334054 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531334054 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 608) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 16, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 609) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 16, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 610) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 17, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 611) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 17, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531334054 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 Building ZINC001531334054 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531334054 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 608) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 16, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 609) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 16, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 610) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 17, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 611) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C) `ZINC001531334054.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531334054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531334054 none CN1c2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 17, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531334054 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531334054 Building ZINC001531397406 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531397406 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/612 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531397406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531397406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531397406 none O=C(N1CCN(c2cc(Cl)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 12, 20, 20, 20, 20, 43, 43, 43, 28, 43, 43, 43, 20, 20, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 43, 38, 43, 20, 20, 20, 20, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/613 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531397406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531397406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531397406 none O=C(N1CCN(c2cc(Cl)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 12, 20, 20, 20, 20, 45, 45, 45, 31, 45, 45, 45, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 45, 45, 45, 20, 20, 20, 20, 3, 1, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531397406 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 Building ZINC001531397406 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531397406 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 612) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531397406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531397406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531397406 none O=C(N1CCN(c2cc(Cl)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 12, 20, 20, 20, 20, 43, 43, 43, 28, 43, 43, 43, 20, 20, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 43, 38, 43, 20, 20, 20, 20, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 613) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531397406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531397406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531397406 none O=C(N1CCN(c2cc(Cl)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 12, 20, 20, 20, 20, 45, 45, 45, 31, 45, 45, 45, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 45, 45, 45, 20, 20, 20, 20, 3, 1, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531397406 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531397406 Building ZINC001531409338 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531409338 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/614 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1) `ZINC001531409338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531409338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531409338 none CCCc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 6, 4, 15, 15, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/615 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1) `ZINC001531409338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531409338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531409338 none CCCc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 5, 20, 20, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531409338 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 Building ZINC001531409338 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531409338 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 614) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1) `ZINC001531409338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531409338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531409338 none CCCc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 6, 4, 15, 15, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 615) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1) `ZINC001531409338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531409338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531409338 none CCCc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 5, 20, 20, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531409338 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409338 Building ZINC001531409339 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531409339 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/616 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1) `ZINC001531409339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531409339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531409339 none CCCc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 10, 20, 20, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/617 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1) `ZINC001531409339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531409339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531409339 none CCCc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 8, 8, 15, 15, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531409339 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 Building ZINC001531409339 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531409339 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 616) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1) `ZINC001531409339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531409339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531409339 none CCCc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 10, 20, 20, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 617) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1) `ZINC001531409339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531409339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531409339 none CCCc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cccs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 8, 8, 15, 15, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531409339 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531409339 Building ZINC001531431900 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531431900 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/618 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(c2ccccc2Cl)csc1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC001531431900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531431900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531431900 none COC(=O)c1c(c2ccccc2Cl)csc1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 10, 30, 10, 10, 10, 26, 26, 20, 26, 26, 26, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 30, 30, 30, 26, 26, 20, 26, 10, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/619 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(c2ccccc2Cl)csc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC001531431900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531431900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531431900 none COC(=O)c1c(c2ccccc2Cl)csc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 10, 29, 10, 10, 10, 27, 27, 10, 27, 27, 27, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 29, 29, 29, 27, 27, 20, 27, 10, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531431900 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 Building ZINC001531431900 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531431900 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 618) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(c2ccccc2Cl)csc1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC001531431900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531431900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531431900 none COC(=O)c1c(c2ccccc2Cl)csc1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 10, 30, 10, 10, 10, 26, 26, 20, 26, 26, 26, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 30, 30, 30, 26, 26, 20, 26, 10, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 619) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(c2ccccc2Cl)csc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC001531431900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531431900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531431900 none COC(=O)c1c(c2ccccc2Cl)csc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 10, 29, 10, 10, 10, 27, 27, 10, 27, 27, 27, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 29, 29, 29, 27, 27, 20, 27, 10, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531431900 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531431900 Building ZINC001531496404 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531496404 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/620 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3cccc(C(F)(F)F)c3)s2)cc1Cl) `ZINC001531496404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531496404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531496404 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3cccc(C(F)(F)F)c3)s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 18, 5, 18, 18, 18, 18, 18, 18, 5, 6, 6, 6, 14, 14, 14, 6, 6, 3, 18, 18, 5, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/621 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3cccc(C(F)(F)F)c3)s2)cc1Cl) `ZINC001531496404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531496404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531496404 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3cccc(C(F)(F)F)c3)s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 18, 10, 18, 18, 18, 18, 18, 18, 5, 6, 6, 6, 14, 14, 14, 6, 6, 3, 18, 18, 10, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531496404 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 Building ZINC001531496404 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531496404 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 620) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3cccc(C(F)(F)F)c3)s2)cc1Cl) `ZINC001531496404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531496404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531496404 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3cccc(C(F)(F)F)c3)s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 18, 5, 18, 18, 18, 18, 18, 18, 5, 6, 6, 6, 14, 14, 14, 6, 6, 3, 18, 18, 5, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 621) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3cccc(C(F)(F)F)c3)s2)cc1Cl) `ZINC001531496404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531496404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531496404 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3cccc(C(F)(F)F)c3)s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 18, 10, 18, 18, 18, 18, 18, 18, 5, 6, 6, 6, 14, 14, 14, 6, 6, 3, 18, 18, 10, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531496404 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531496404 Building ZINC001531500511 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531500511 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/622 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001531500511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531500511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001531500511 none O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 5, 7, 7, 7, 7, 22, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/623 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001531500511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531500511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001531500511 none O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 5, 7, 7, 7, 7, 22, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531500511 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 Building ZINC001531500511 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531500511 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 622) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001531500511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531500511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001531500511 none O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 5, 7, 7, 7, 7, 22, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 623) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001531500511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531500511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001531500511 none O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 5, 7, 7, 7, 7, 22, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531500511 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531500511 Building ZINC001531506776 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531506776 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/624 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccccc1Cl) `ZINC001531506776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531506776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001531506776 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 26, 26, 15, 26, 26, 26, 15, 15, 15, 15, 15, 4, 9, 9, 8, 26, 26, 15, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/625 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccccc1Cl) `ZINC001531506776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531506776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001531506776 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26, 15, 26, 26, 26, 15, 15, 15, 15, 15, 4, 8, 8, 8, 26, 26, 15, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531506776 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 Building ZINC001531506776 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531506776 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 624) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccccc1Cl) `ZINC001531506776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531506776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001531506776 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 26, 26, 15, 26, 26, 26, 15, 15, 15, 15, 15, 4, 9, 9, 8, 26, 26, 15, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 625) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccccc1Cl) `ZINC001531506776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531506776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001531506776 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26, 15, 26, 26, 26, 15, 15, 15, 15, 15, 4, 8, 8, 8, 26, 26, 15, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531506776 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531506776 Building ZINC001531507257 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531507257 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/626 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(Cl)cc1) `ZINC001531507257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531507257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531507257 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 2, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 8, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 85 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/627 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(Cl)cc1) `ZINC001531507257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531507257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531507257 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 8, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 105 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531507257 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 Building ZINC001531507257 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531507257 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 626) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(Cl)cc1) `ZINC001531507257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531507257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531507257 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 2, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 8, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 85 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 627) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(Cl)cc1) `ZINC001531507257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531507257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531507257 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 8, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 105 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531507257 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507257 Building ZINC001531507725 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531507725 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/628 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cnn1c1cccc(C(F)(F)F)c1) `ZINC001531507725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531507725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001531507725 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cnn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 28, 28, 18, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 9, 9, 8, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/629 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cnn1c1cccc(C(F)(F)F)c1) `ZINC001531507725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531507725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001531507725 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cnn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 29, 29, 8, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 4, 9, 9, 8, 29, 29, 15, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531507725 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 Building ZINC001531507725 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531507725 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 628) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cnn1c1cccc(C(F)(F)F)c1) `ZINC001531507725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531507725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001531507725 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cnn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 28, 28, 18, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 9, 9, 8, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 629) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cnn1c1cccc(C(F)(F)F)c1) `ZINC001531507725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531507725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001531507725 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cnn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 29, 29, 8, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 4, 9, 9, 8, 29, 29, 15, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531507725 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531507725 Building ZINC001531535496 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531535496 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/630 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1) `ZINC001531535496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531535496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001531535496 none Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 39, 39, 39, 39, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 45, 45, 45, 45, 45, 39, 39, 11, 11, 2, 4, 4, 45] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/631 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1) `ZINC001531535496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531535496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001531535496 none Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 39, 39, 39, 39, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 44, 44, 44, 44, 44, 39, 39, 11, 11, 2, 4, 4, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531535496 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 Building ZINC001531535496 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531535496 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 630) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1) `ZINC001531535496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531535496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001531535496 none Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 39, 39, 39, 39, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 45, 45, 45, 45, 45, 39, 39, 11, 11, 2, 4, 4, 45] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 631) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1) `ZINC001531535496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531535496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001531535496 none Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 39, 39, 39, 39, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 39, 44, 44, 44, 44, 44, 39, 39, 11, 11, 2, 4, 4, 44] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531535496 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531535496 Building ZINC001531540174 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531540174 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/632 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCN(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001531540174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531540174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531540174 none Cc1ccc(CCN(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 9, 4, 9, 22, 26, 26, 26, 26, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 26, 26, 26, 6, 6, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/633 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCN(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001531540174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531540174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531540174 none Cc1ccc(CCN(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 9, 4, 9, 21, 24, 24, 24, 24, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 21, 24, 24, 24, 7, 7, 14, 14] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531540174 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 Building ZINC001531540174 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531540174 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 632) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCN(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001531540174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531540174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531540174 none Cc1ccc(CCN(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 9, 4, 9, 22, 26, 26, 26, 26, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 26, 26, 26, 6, 6, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 633) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCN(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001531540174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531540174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531540174 none Cc1ccc(CCN(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 9, 4, 9, 21, 24, 24, 24, 24, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 21, 24, 24, 24, 7, 7, 14, 14] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531540174 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531540174 Building ZINC001531551920 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531551920 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/634 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2ccccc2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531551920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531551920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531551920 none CCOC(=O)c1sc(c2ccccc2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 13, 7, 13, 7, 7, 7, 7, 24, 24, 7, 24, 24, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 24, 24, 7, 24, 24, 7, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/635 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2ccccc2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531551920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531551920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531551920 none CCOC(=O)c1sc(c2ccccc2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 13, 7, 13, 7, 7, 7, 7, 24, 24, 7, 24, 24, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 24, 24, 7, 24, 24, 7, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531551920 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 Building ZINC001531551920 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531551920 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 634) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2ccccc2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531551920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531551920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531551920 none CCOC(=O)c1sc(c2ccccc2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 13, 7, 13, 7, 7, 7, 7, 24, 24, 7, 24, 24, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 24, 24, 7, 24, 24, 7, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 635) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2ccccc2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531551920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531551920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531551920 none CCOC(=O)c1sc(c2ccccc2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 13, 7, 13, 7, 7, 7, 7, 24, 24, 7, 24, 24, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 24, 24, 7, 24, 24, 7, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531551920 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531551920 Building ZINC001531585116 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531585116 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/636 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OC(F)(F)F)cc1) `ZINC001531585116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531585116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531585116 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 14, 14, 6, 9, 50, 50, 50, 50, 14, 14, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 10, 11, 12, 2, 14, 13, 4, 15, 42] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/637 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OC(F)(F)F)cc1) `ZINC001531585116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531585116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531585116 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 6, 9, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 10, 11, 12, 2, 14, 13, 4, 15, 42] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531585116 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 Building ZINC001531585116 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531585116 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 636) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OC(F)(F)F)cc1) `ZINC001531585116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531585116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531585116 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 14, 14, 6, 9, 50, 50, 50, 50, 14, 14, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 10, 11, 12, 2, 14, 13, 4, 15, 42] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 637) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OC(F)(F)F)cc1) `ZINC001531585116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531585116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001531585116 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 6, 9, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 10, 11, 12, 2, 14, 13, 4, 15, 42] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531585116 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531585116 Building ZINC001531590551 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531590551 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/638 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC) `ZINC001531590551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531590551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001531590551 none CCOc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 7, 7, 7, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 3, 3, 3, 7, 7, 7, 22, 24, 26, 26, 26, 26, 26, 7, 7, 3, 6, 6, 10, 10, 10, 6, 3, 3, 3, 3, 3, 3, 3, 7, 24, 24, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/639 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC) `ZINC001531590551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531590551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001531590551 none CCOc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 4, 4, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 2, 2, 2, 4, 4, 4, 19, 24, 18, 18, 18, 18, 18, 4, 4, 2, 6, 6, 10, 10, 10, 6, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531590551 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 Building ZINC001531590551 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531590551 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 638) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC) `ZINC001531590551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531590551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001531590551 none CCOc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 7, 7, 7, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 3, 3, 3, 7, 7, 7, 22, 24, 26, 26, 26, 26, 26, 7, 7, 3, 6, 6, 10, 10, 10, 6, 3, 3, 3, 3, 3, 3, 3, 7, 24, 24, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 639) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC) `ZINC001531590551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531590551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001531590551 none CCOc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 4, 4, 4, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 2, 2, 2, 4, 4, 4, 19, 24, 18, 18, 18, 18, 18, 4, 4, 2, 6, 6, 10, 10, 10, 6, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531590551 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590551 Building ZINC001531590552 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531590552 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/640 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC) `ZINC001531590552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531590552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001531590552 none CCOc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 4, 4, 4, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 9, 5, 5, 5, 2, 2, 2, 4, 4, 4, 20, 25, 19, 19, 19, 19, 19, 4, 4, 2, 5, 5, 9, 9, 9, 5, 2, 2, 2, 2, 2, 2, 2, 4, 25, 25, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/641 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC) `ZINC001531590552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531590552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001531590552 none CCOc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 21, 7, 7, 7, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 3, 3, 3, 7, 7, 7, 22, 25, 23, 23, 23, 23, 23, 7, 7, 3, 5, 5, 10, 10, 10, 5, 3, 3, 3, 3, 3, 3, 3, 7, 25, 25, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531590552 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 Building ZINC001531590552 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531590552 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 640) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC) `ZINC001531590552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531590552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001531590552 none CCOc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 4, 4, 4, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 9, 5, 5, 5, 2, 2, 2, 4, 4, 4, 20, 25, 19, 19, 19, 19, 19, 4, 4, 2, 5, 5, 9, 9, 9, 5, 2, 2, 2, 2, 2, 2, 2, 4, 25, 25, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 641) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC) `ZINC001531590552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531590552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001531590552 none CCOc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C(C)C)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 21, 7, 7, 7, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 3, 3, 3, 7, 7, 7, 22, 25, 23, 23, 23, 23, 23, 7, 7, 3, 5, 5, 10, 10, 10, 5, 3, 3, 3, 3, 3, 3, 3, 7, 25, 25, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531590552 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531590552 Building ZINC001531606113 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531606113 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/642 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)ccn2)c1C) `ZINC001531606113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531606113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531606113 none Cc1cccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)ccn2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 5, 5, 1, 1, 1, 14, 14, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/643 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)ccn2)c1C) `ZINC001531606113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531606113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531606113 none Cc1cccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)ccn2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 5, 5, 1, 1, 1, 14, 14, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531606113 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 Building ZINC001531606113 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531606113 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 642) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)ccn2)c1C) `ZINC001531606113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531606113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531606113 none Cc1cccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)ccn2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 5, 5, 1, 1, 1, 14, 14, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 643) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)ccn2)c1C) `ZINC001531606113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531606113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531606113 none Cc1cccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)ccn2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 5, 5, 1, 1, 1, 14, 14, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531606113 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531606113 Building ZINC001531619315 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531619315 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/644 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Oc1ncccc1Br) `ZINC001531619315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531619315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531619315 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Oc1ncccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 41, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 11, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/645 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Oc1ncccc1Br) `ZINC001531619315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531619315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531619315 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Oc1ncccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 40, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 11, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531619315 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 Building ZINC001531619315 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531619315 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 644) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Oc1ncccc1Br) `ZINC001531619315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531619315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531619315 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Oc1ncccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 41, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 11, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 645) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Oc1ncccc1Br) `ZINC001531619315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531619315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531619315 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Oc1ncccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 40, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 11, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531619315 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531619315 Building ZINC001531633745 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531633745 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/646 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)C)CC1) `ZINC001531633745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531633745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001531633745 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 7, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 1, 5, 6, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/647 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)C)CC1) `ZINC001531633745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531633745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001531633745 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 8, 9, 9, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 52 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531633745 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 Building ZINC001531633745 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531633745 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 646) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)C)CC1) `ZINC001531633745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531633745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001531633745 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 7, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 1, 5, 6, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 647) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)C)CC1) `ZINC001531633745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531633745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001531633745 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 8, 9, 9, 9, 9, 9, 9, 9, 10, 10, 9, 9, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 52 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531633745 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633745 Building ZINC001531633746 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531633746 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/648 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)C)CC1) `ZINC001531633746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531633746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001531633746 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 6, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 9, 13, 13, 9, 9, 3, 3, 3, 18, 18, 10, 18, 3, 3, 3, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 88 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/649 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)C)CC1) `ZINC001531633746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531633746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001531633746 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 13, 13, 7, 13, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531633746 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 Building ZINC001531633746 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531633746 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 648) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)C)CC1) `ZINC001531633746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531633746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001531633746 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 6, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 9, 13, 13, 9, 9, 3, 3, 3, 18, 18, 10, 18, 3, 3, 3, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 88 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 649) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)C)CC1) `ZINC001531633746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531633746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001531633746 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 8, 8, 9, 9, 8, 8, 2, 2, 2, 13, 13, 7, 13, 2, 2, 2, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 58 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531633746 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531633746 Building ZINC001531650764 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531650764 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/650 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)cc1) `ZINC001531650764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531650764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001531650764 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 23, 29, 29, 29, 50, 50, 29, 29, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 23, 23, 29, 50, 50, 50, 50, 6, 6, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/651 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)cc1) `ZINC001531650764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531650764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001531650764 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 23, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 23, 23, 30, 50, 50, 50, 50, 6, 6, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531650764 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 Building ZINC001531650764 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531650764 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 650) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)cc1) `ZINC001531650764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531650764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001531650764 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 23, 29, 29, 29, 50, 50, 29, 29, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 23, 23, 29, 50, 50, 50, 50, 6, 6, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 651) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)cc1) `ZINC001531650764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531650764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001531650764 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CNC(=O)c3ccc(C(F)(F)F)cc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 23, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 23, 23, 30, 50, 50, 50, 50, 6, 6, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531650764 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531650764 Building ZINC001531659583 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531659583 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/652 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)c(Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531659583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531659583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531659583 none O=C(Nc1ccc(OC(F)F)c(Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 3, 4, 25, 31, 31, 8, 8, 19, 23, 23, 19, 23, 23, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 31, 19, 19, 23, 23, 19, 23, 23, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/653 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)c(Cc2ccccc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531659583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531659583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531659583 none O=C(Nc1ccc(OC(F)F)c(Cc2ccccc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 29, 32, 32, 8, 8, 19, 23, 23, 20, 23, 23, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 19, 19, 23, 23, 20, 23, 23, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531659583 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 Building ZINC001531659583 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531659583 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 652) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)c(Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531659583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531659583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531659583 none O=C(Nc1ccc(OC(F)F)c(Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 3, 4, 25, 31, 31, 8, 8, 19, 23, 23, 19, 23, 23, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 31, 19, 19, 23, 23, 19, 23, 23, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 653) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)c(Cc2ccccc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531659583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531659583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531659583 none O=C(Nc1ccc(OC(F)F)c(Cc2ccccc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 29, 32, 32, 8, 8, 19, 23, 23, 20, 23, 23, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 32, 19, 19, 23, 23, 20, 23, 23, 8, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531659583 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531659583 Building ZINC001531681210 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531681210 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/654 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C(F)(F)F)cc2C2CC2)cc1) `ZINC001531681210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531681210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531681210 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C(F)(F)F)cc2C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 47, 47, 10, 10, 3, 3, 3, 3, 3, 3, 3, 4, 10, 10, 25, 47, 47, 47, 47, 47, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/655 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C(F)(F)F)cc2C2CC2)cc1) `ZINC001531681210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531681210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531681210 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C(F)(F)F)cc2C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 48, 48, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 37, 48, 48, 48, 48, 48, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531681210 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 Building ZINC001531681210 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531681210 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 654) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C(F)(F)F)cc2C2CC2)cc1) `ZINC001531681210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531681210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531681210 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C(F)(F)F)cc2C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 47, 47, 10, 10, 3, 3, 3, 3, 3, 3, 3, 4, 10, 10, 25, 47, 47, 47, 47, 47, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 655) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C(F)(F)F)cc2C2CC2)cc1) `ZINC001531681210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531681210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531681210 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C(F)(F)F)cc2C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 48, 48, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 37, 48, 48, 48, 48, 48, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531681210 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531681210 Building ZINC001531704505 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531704505 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/656 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Cl)cc1) `ZINC001531704505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531704505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001531704505 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 27, 31, 15, 8, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 8, 9, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 31, 31, 31, 31, 31, 15, 15, 15, 15, 5, 5, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/657 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Cl)cc1) `ZINC001531704505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531704505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001531704505 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 16, 27, 30, 15, 8, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 8, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 30, 30, 30, 30, 30, 16, 16, 15, 15, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 164 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531704505 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 Building ZINC001531704505 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531704505 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 656) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Cl)cc1) `ZINC001531704505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531704505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001531704505 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 27, 31, 15, 8, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 8, 9, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 31, 31, 31, 31, 31, 15, 15, 15, 15, 5, 5, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 657) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Cl)cc1) `ZINC001531704505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531704505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001531704505 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 16, 27, 30, 15, 8, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 8, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 30, 30, 30, 30, 30, 16, 16, 15, 15, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 164 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531704505 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531704505 Building ZINC001531761902 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531761902 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/658 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)cc(C)c1) `ZINC001531761902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531761902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531761902 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)cc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 13, 13, 13, 8, 13, 13, 13, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 8, 8, 13, 13, 13, 13, 8, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/659 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)cc(C)c1) `ZINC001531761902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531761902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531761902 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)cc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 12, 12, 7, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 3, 3, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531761902 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 Building ZINC001531761902 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531761902 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 658) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)cc(C)c1) `ZINC001531761902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531761902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531761902 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)cc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 13, 13, 13, 8, 13, 13, 13, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 8, 8, 13, 13, 13, 13, 8, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 659) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)cc(C)c1) `ZINC001531761902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531761902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531761902 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)cc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 7, 12, 12, 12, 7, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 3, 3, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531761902 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531761902 Building ZINC001531798731 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531798731 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/660 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/660' -> `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]1CCOc2c(Cl)c(Cl)ccc21) `ZINC001531798731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531798731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531798731 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOc2c(Cl)c(Cl)ccc21 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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 4, 6, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/661 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/661' -> `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]1CCOc2c(Cl)c(Cl)ccc21) `ZINC001531798731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531798731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531798731 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOc2c(Cl)c(Cl)ccc21 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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 6, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 6, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531798731 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 Building ZINC001531798731 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531798731 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 660) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOc2c(Cl)c(Cl)ccc21) `ZINC001531798731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531798731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531798731 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOc2c(Cl)c(Cl)ccc21 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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 4, 6, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 661) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOc2c(Cl)c(Cl)ccc21) `ZINC001531798731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531798731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531798731 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOc2c(Cl)c(Cl)ccc21 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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 6, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 6, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531798731 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798731 Building ZINC001531798927 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531798927 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/662 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/662' -> `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]1CCOc2c(Cl)c(Cl)ccc21) `ZINC001531798927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531798927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531798927 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOc2c(Cl)c(Cl)ccc21 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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4, 8, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/663 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/663' -> `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]1CCOc2c(Cl)c(Cl)ccc21) `ZINC001531798927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531798927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531798927 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOc2c(Cl)c(Cl)ccc21 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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 6, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531798927 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 Building ZINC001531798927 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531798927 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 662) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOc2c(Cl)c(Cl)ccc21) `ZINC001531798927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531798927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531798927 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOc2c(Cl)c(Cl)ccc21 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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4, 8, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 663) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOc2c(Cl)c(Cl)ccc21) `ZINC001531798927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531798927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001531798927 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOc2c(Cl)c(Cl)ccc21 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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 6, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531798927 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531798927 Building ZINC001531808051 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531808051 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/664 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc3ccccc32)cc1) `ZINC001531808051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531808051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001531808051 none COc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 21, 22, 22, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 5, 6, 16, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 3, 6, 6, 16, 16, 16, 6, 7, 7, 7, 7, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/665 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc3ccccc32)cc1) `ZINC001531808051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531808051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001531808051 none COc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 7, 22, 22, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 16, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 3, 6, 6, 16, 16, 16, 6, 7, 7, 7, 7, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531808051 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 Building ZINC001531808051 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531808051 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 664) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc3ccccc32)cc1) `ZINC001531808051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531808051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001531808051 none COc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 21, 22, 22, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 5, 6, 16, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 3, 6, 6, 16, 16, 16, 6, 7, 7, 7, 7, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 665) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc3ccccc32)cc1) `ZINC001531808051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531808051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001531808051 none COc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 7, 22, 22, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 16, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 3, 6, 6, 16, 16, 16, 6, 7, 7, 7, 7, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531808051 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808051 Building ZINC001531808240 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531808240 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/666 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2c2ccccc2OC)cc1Cl) `ZINC001531808240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531808240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001531808240 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2c2ccccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 16, 20, 20, 20, 24, 5, 5, 5, 9, 9, 9, 5, 5, 3, 6, 6, 6, 6, 20, 20, 20, 20, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/667 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2c2ccccc2OC)cc1Cl) `ZINC001531808240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531808240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001531808240 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2c2ccccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 16, 20, 20, 20, 24, 5, 5, 5, 9, 9, 9, 5, 5, 3, 6, 6, 6, 6, 20, 20, 20, 20, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531808240 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 Building ZINC001531808240 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531808240 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 666) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2c2ccccc2OC)cc1Cl) `ZINC001531808240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531808240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001531808240 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2c2ccccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 16, 20, 20, 20, 24, 5, 5, 5, 9, 9, 9, 5, 5, 3, 6, 6, 6, 6, 20, 20, 20, 20, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 667) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2c2ccccc2OC)cc1Cl) `ZINC001531808240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531808240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001531808240 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccccc3n2c2ccccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 16, 20, 20, 20, 24, 5, 5, 5, 9, 9, 9, 5, 5, 3, 6, 6, 6, 6, 20, 20, 20, 20, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531808240 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531808240 Building ZINC001531817906 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531817906 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/668 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1CN(Cc1c(C)noc1C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531817906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531817906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531817906 none Cc1noc(C)c1CN(Cc1c(C)noc1C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 8, 5, 1, 1, 5, 8, 12, 1, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 23, 12, 4, 12, 17, 29, 29, 29, 29, 29, 29, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 23, 23, 17, 17, 29, 29, 29, 29, 29, 29, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/669 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1CN(Cc1c(C)noc1C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531817906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531817906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531817906 none Cc1noc(C)c1CN(Cc1c(C)noc1C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 8, 5, 1, 1, 5, 8, 12, 1, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 23, 12, 4, 12, 17, 29, 29, 29, 29, 29, 29, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 30, 30, 30, 30, 23, 23, 17, 17, 29, 29, 29, 29, 29, 29, 2, 1, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531817906 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 Building ZINC001531817906 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531817906 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 668) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1CN(Cc1c(C)noc1C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531817906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531817906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531817906 none Cc1noc(C)c1CN(Cc1c(C)noc1C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 8, 5, 1, 1, 5, 8, 12, 1, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 23, 12, 4, 12, 17, 29, 29, 29, 29, 29, 29, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 23, 23, 17, 17, 29, 29, 29, 29, 29, 29, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 669) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1CN(Cc1c(C)noc1C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531817906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531817906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001531817906 none Cc1noc(C)c1CN(Cc1c(C)noc1C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 8, 5, 1, 1, 5, 8, 12, 1, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 23, 12, 4, 12, 17, 29, 29, 29, 29, 29, 29, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 30, 30, 30, 30, 23, 23, 17, 17, 29, 29, 29, 29, 29, 29, 2, 1, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531817906 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531817906 Building ZINC001531818235 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531818235 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/670 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(Oc3ccccc3)c2)ns1) `ZINC001531818235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531818235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531818235 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(Oc3ccccc3)c2)ns1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 40, 50, 50, 43, 50, 50, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 50, 50, 44, 50, 50, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/671 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(Oc3ccccc3)c2)ns1) `ZINC001531818235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531818235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531818235 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(Oc3ccccc3)c2)ns1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 40, 50, 50, 40, 50, 50, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 50, 50, 40, 50, 50, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531818235 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 Building ZINC001531818235 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531818235 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 670) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1nc(c2cccc(Oc3ccccc3)c2)ns1) `ZINC001531818235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531818235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531818235 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(Oc3ccccc3)c2)ns1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 40, 50, 50, 43, 50, 50, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 50, 50, 44, 50, 50, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 671) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1nc(c2cccc(Oc3ccccc3)c2)ns1) `ZINC001531818235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531818235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531818235 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2cccc(Oc3ccccc3)c2)ns1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 40, 50, 50, 40, 50, 50, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 50, 50, 40, 50, 50, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531818235 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531818235 Building ZINC001531819206 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531819206 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/672 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)Nc1c(Cl)cccc1Cl)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531819206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531819206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001531819206 none CCN(CC(=O)Nc1c(Cl)cccc1Cl)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 11, 27, 27, 27, 41, 41, 41, 35, 41, 41, 41, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 27, 41, 35, 41, 3, 1, 3] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/673 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)Nc1c(Cl)cccc1Cl)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531819206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531819206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001531819206 none CCN(CC(=O)Nc1c(Cl)cccc1Cl)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 4, 8, 12, 27, 27, 27, 40, 40, 40, 35, 40, 40, 40, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 27, 40, 40, 40, 3, 1, 3] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531819206 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 Building ZINC001531819206 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531819206 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 672) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)Nc1c(Cl)cccc1Cl)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531819206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531819206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001531819206 none CCN(CC(=O)Nc1c(Cl)cccc1Cl)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 11, 27, 27, 27, 41, 41, 41, 35, 41, 41, 41, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 27, 41, 35, 41, 3, 1, 3] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 673) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)Nc1c(Cl)cccc1Cl)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001531819206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531819206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001531819206 none CCN(CC(=O)Nc1c(Cl)cccc1Cl)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 4, 8, 12, 27, 27, 27, 40, 40, 40, 35, 40, 40, 40, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 27, 40, 40, 40, 3, 1, 3] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531819206 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531819206 Building ZINC001531832779 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531832779 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/674 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1) `ZINC001531832779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531832779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531832779 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 11, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 11, 19, 19, 19, 19, 2] 50 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/675 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1) `ZINC001531832779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531832779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531832779 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 10, 18, 18, 18, 18, 1] 50 rigid atoms, others: [17, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 46, 39, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531832779 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 Building ZINC001531832779 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531832779 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 674) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1) `ZINC001531832779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531832779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531832779 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 11, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 11, 19, 19, 19, 19, 2] 50 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 675) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1) `ZINC001531832779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531832779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001531832779 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 10, 18, 18, 18, 18, 1] 50 rigid atoms, others: [17, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 46, 39, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531832779 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531832779 Building ZINC001531886276 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531886276 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/676 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(C)c(C)c1) `ZINC001531886276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531886276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531886276 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 8, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/677 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(C)c(C)c1) `ZINC001531886276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531886276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531886276 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 7, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 6, 6, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531886276 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 Building ZINC001531886276 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531886276 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 676) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(C)c(C)c1) `ZINC001531886276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531886276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531886276 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 8, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 677) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(C)c(C)c1) `ZINC001531886276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531886276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531886276 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 7, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 6, 6, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531886276 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531886276 Building ZINC001531908788 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531908788 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/678 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCCC2)cn1) `ZINC001531908788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531908788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001531908788 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 10, 10, 1, 1, 1, 1, 4, 4, 7, 15, 20, 20, 16, 19, 20, 20, 15, 15, 15, 15, 15, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 4, 20, 20, 20, 20, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/679 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCCC2)cn1) `ZINC001531908788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531908788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001531908788 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 17, 9, 9, 1, 1, 1, 1, 5, 5, 8, 15, 21, 21, 16, 21, 21, 21, 15, 15, 15, 15, 15, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531908788 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 Building ZINC001531908788 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531908788 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 678) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCCC2)cn1) `ZINC001531908788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531908788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001531908788 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 10, 10, 1, 1, 1, 1, 4, 4, 7, 15, 20, 20, 16, 19, 20, 20, 15, 15, 15, 15, 15, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 4, 20, 20, 20, 20, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 679) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCCC2)cn1) `ZINC001531908788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531908788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001531908788 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 17, 9, 9, 1, 1, 1, 1, 5, 5, 8, 15, 21, 21, 16, 21, 21, 21, 15, 15, 15, 15, 15, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531908788 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531908788 Building ZINC001531915482 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531915482 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/680 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2sccc2[C@H]1c1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001531915482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531915482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531915482 none O=C(N1CCc2sccc2[C@H]1c1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 31, 31, 31, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/681 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2sccc2[C@H]1c1cccs1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001531915482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531915482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531915482 none O=C(N1CCc2sccc2[C@H]1c1cccs1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 30, 30, 30, 30, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 30, 30, 30, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531915482 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 Building ZINC001531915482 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531915482 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 680) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2sccc2[C@H]1c1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001531915482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531915482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531915482 none O=C(N1CCc2sccc2[C@H]1c1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 31, 31, 31, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 681) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2sccc2[C@H]1c1cccs1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001531915482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531915482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531915482 none O=C(N1CCc2sccc2[C@H]1c1cccs1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 30, 30, 30, 30, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 30, 30, 30, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531915482 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915482 Building ZINC001531915483 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531915483 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/682 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2sccc2[C@@H]1c1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001531915483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531915483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531915483 none O=C(N1CCc2sccc2[C@@H]1c1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 31, 31, 31, 31, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 31, 31, 31, 7, 7] 50 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/683 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2sccc2[C@@H]1c1cccs1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001531915483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531915483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531915483 none O=C(N1CCc2sccc2[C@@H]1c1cccs1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 33, 33, 33, 33, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 33, 33, 33, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531915483 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 Building ZINC001531915483 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531915483 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 682) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2sccc2[C@@H]1c1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001531915483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531915483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531915483 none O=C(N1CCc2sccc2[C@@H]1c1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 31, 31, 31, 31, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 31, 31, 31, 7, 7] 50 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 683) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2sccc2[C@@H]1c1cccs1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001531915483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531915483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001531915483 none O=C(N1CCc2sccc2[C@@H]1c1cccs1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 33, 33, 33, 33, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 33, 33, 33, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531915483 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531915483 Building ZINC001531919020 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531919020 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/684 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c1C) `ZINC001531919020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531919020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531919020 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 44, 44, 44, 44, 44, 44, 11, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 44, 44, 44, 44, 11, 3, 3, 3, 3, 3, 3, 38, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/685 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c1C) `ZINC001531919020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531919020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531919020 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 45, 45, 45, 45, 45, 45, 11, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 45, 45, 45, 45, 11, 3, 3, 3, 3, 3, 3, 38, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531919020 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 Building ZINC001531919020 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531919020 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 684) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c1C) `ZINC001531919020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531919020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531919020 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 44, 44, 44, 44, 44, 44, 11, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 44, 44, 44, 44, 11, 3, 3, 3, 3, 3, 3, 38, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 685) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c1C) `ZINC001531919020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531919020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001531919020 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 45, 45, 45, 45, 45, 45, 11, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 45, 45, 45, 45, 11, 3, 3, 3, 3, 3, 3, 38, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531919020 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531919020 Building ZINC001531932846 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531932846 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/686 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531932846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932846 none O=C(Nc1nc([C@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 29, 29, 29, 29, 29, 29, 29, 29, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/687 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531932846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932846 none O=C(Nc1nc([C@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 30, 30, 30, 30, 30, 30, 30, 30, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531932846 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 Building ZINC001531932846 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531932846 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 686) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531932846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932846 none O=C(Nc1nc([C@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 29, 29, 29, 29, 29, 29, 29, 29, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 687) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531932846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932846 none O=C(Nc1nc([C@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 30, 30, 30, 30, 30, 30, 30, 30, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531932846 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932846 Building ZINC001531932848 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531932848 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/688 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531932848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932848 none O=C(Nc1nc([C@@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 30, 30, 30, 30, 30, 30, 30, 30, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/689 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531932848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932848 none O=C(Nc1nc([C@@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 29, 29, 29, 29, 29, 29, 29, 29, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531932848 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 Building ZINC001531932848 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531932848 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 688) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531932848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932848 none O=C(Nc1nc([C@@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 30, 30, 30, 30, 30, 30, 30, 30, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 689) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531932848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932848 none O=C(Nc1nc([C@@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 29, 29, 29, 29, 29, 29, 29, 29, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531932848 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932848 Building ZINC001531932849 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531932849 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/690 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531932849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932849 none O=C(Nc1nc([C@@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 27, 27, 27, 27, 27, 27, 27, 27, 5, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/691 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531932849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932849 none O=C(Nc1nc([C@@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 3, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 6, 6, 5, 6, 6, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531932849 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 Building ZINC001531932849 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531932849 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 690) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531932849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932849 none O=C(Nc1nc([C@@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 27, 27, 27, 27, 27, 27, 27, 27, 5, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 691) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531932849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932849 none O=C(Nc1nc([C@@H]2CCC[C@@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 3, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 6, 6, 5, 6, 6, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531932849 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932849 Building ZINC001531932851 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531932851 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/692 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531932851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932851 none O=C(Nc1nc([C@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 26, 26, 26, 26, 26, 26, 26, 26, 5, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/693 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531932851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932851 none O=C(Nc1nc([C@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 26, 26, 26, 26, 26, 26, 26, 26, 5, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531932851 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 Building ZINC001531932851 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531932851 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 692) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531932851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932851 none O=C(Nc1nc([C@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 26, 26, 26, 26, 26, 26, 26, 26, 5, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 693) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc([C@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001531932851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531932851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531932851 none O=C(Nc1nc([C@H]2CCC[C@H](C(F)(F)F)C2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 26, 26, 26, 26, 26, 26, 26, 26, 5, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531932851 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531932851 Building ZINC001531948642 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531948642 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/694 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 21, 21, 21, 5, 5, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 96 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/695 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 19, 19, 22, 22, 22, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 19, 19, 19, 19, 30, 30, 30, 30, 30, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/696 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/696' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 21, 21, 21, 5, 5, 1, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/697 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/697' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 20, 20, 20, 20, 20, 31, 31, 20, 31, 31, 20, 20, 23, 23, 23, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 20, 20, 20, 20, 31, 31, 20, 31, 31, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531948642 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 Building ZINC001531948642 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531948642 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 694) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 21, 21, 21, 5, 5, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 96 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 695) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 19, 19, 22, 22, 22, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 19, 19, 19, 19, 30, 30, 30, 30, 30, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 696) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 21, 21, 21, 5, 5, 1, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 697) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 20, 20, 20, 20, 20, 31, 31, 20, 31, 31, 20, 20, 23, 23, 23, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 20, 20, 20, 20, 31, 31, 20, 31, 31, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531948642 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 Building ZINC001531948642 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531948642 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 694) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 21, 21, 21, 5, 5, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 96 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 695) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 19, 19, 22, 22, 22, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 19, 19, 19, 19, 30, 30, 30, 30, 30, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 696) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 21, 21, 21, 5, 5, 1, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 697) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 20, 20, 20, 20, 20, 31, 31, 20, 31, 31, 20, 20, 23, 23, 23, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 20, 20, 20, 20, 31, 31, 20, 31, 31, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531948642 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 Building ZINC001531948642 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531948642 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 694) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 21, 21, 21, 5, 5, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 96 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 695) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 19, 19, 22, 22, 22, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 19, 19, 19, 19, 30, 30, 30, 30, 30, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 696) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 21, 21, 21, 5, 5, 1, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 697) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1) `ZINC001531948642.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531948642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001531948642 none CO[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC[C@H](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 20, 20, 20, 20, 20, 31, 31, 20, 31, 31, 20, 20, 23, 23, 23, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 20, 20, 20, 20, 31, 31, 20, 31, 31, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531948642 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531948642 Building ZINC001531975784 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531975784 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/698 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001531975784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531975784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531975784 none CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 16, 6, 6, 6, 15, 15, 6, 11, 24, 15, 15, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 15, 15, 24, 24, 24, 15, 15, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/699 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001531975784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531975784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531975784 none CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 17, 6, 17, 6, 6, 6, 15, 15, 6, 6, 22, 15, 15, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 15, 15, 22, 22, 22, 15, 15, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531975784 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 Building ZINC001531975784 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531975784 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 698) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001531975784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531975784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531975784 none CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 16, 6, 6, 6, 15, 15, 6, 11, 24, 15, 15, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 15, 15, 24, 24, 24, 15, 15, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 699) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001531975784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531975784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001531975784 none CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 17, 6, 17, 6, 6, 6, 15, 15, 6, 6, 22, 15, 15, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 15, 15, 22, 22, 22, 15, 15, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531975784 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531975784 Building ZINC001531985196 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531985196 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/700 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCCc1ccccc1) `ZINC001531985196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531985196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531985196 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCCc1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 14, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/701 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCCc1ccccc1) `ZINC001531985196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531985196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531985196 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCCc1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 14, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531985196 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 Building ZINC001531985196 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531985196 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 700) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCCc1ccccc1) `ZINC001531985196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531985196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531985196 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCCc1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 14, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 701) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCCc1ccccc1) `ZINC001531985196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531985196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001531985196 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCCc1ccccc1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 14, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531985196 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531985196 Building ZINC001531988852 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531988852 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/702 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 14, 49, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/703 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 14, 49, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/704 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/704' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 48, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 48, 48] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/705 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/705' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 48, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 48, 48] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531988852 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 Building ZINC001531988852 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531988852 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 702) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 14, 49, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 703) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 14, 49, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 704) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 48, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 48, 48] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 705) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 48, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 48, 48] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531988852 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 Building ZINC001531988852 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531988852 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 702) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 14, 49, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 703) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 14, 49, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 704) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 48, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 48, 48] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 705) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 48, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 48, 48] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531988852 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 Building ZINC001531988852 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531988852 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 702) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 14, 49, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 703) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 14, 49, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 704) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 48, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 48, 48] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 705) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988852.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531988852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988852 none Cc1cc(Br)cc(C)c1N1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 48, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 48, 48] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531988852 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988852 Building ZINC001531988854 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531988854 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/706 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/707 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/708 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/708' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 4, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/709 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/709' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 4, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531988854 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 Building ZINC001531988854 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531988854 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 706) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 707) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 708) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 4, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 709) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 4, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531988854 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 Building ZINC001531988854 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531988854 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 706) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 707) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 708) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 4, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 709) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 4, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531988854 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 Building ZINC001531988854 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001531988854 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 706) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 707) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 5, 5, 5, 5, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 708) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 4, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 709) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001531988854.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001531988854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001531988854 none Cc1cc(Br)cc(C)c1N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 49, 49, 49, 49, 9, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 4, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531988854 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531988854 Building ZINC001531999706 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531999706 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/710 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3C(F)(F)F)ns2)cc1Cl) `ZINC001531999706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531999706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531999706 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3C(F)(F)F)ns2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 14, 14, 12, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 12, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/711 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3C(F)(F)F)ns2)cc1Cl) `ZINC001531999706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531999706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531999706 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3C(F)(F)F)ns2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 14, 14, 12, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 13, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531999706 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 Building ZINC001531999706 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001531999706 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 710) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3C(F)(F)F)ns2)cc1Cl) `ZINC001531999706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001531999706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531999706 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3C(F)(F)F)ns2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 14, 14, 12, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 12, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 711) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3C(F)(F)F)ns2)cc1Cl) `ZINC001531999706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001531999706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001531999706 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3C(F)(F)F)ns2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 14, 14, 12, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 13, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001531999706 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001531999706 Building ZINC001532043300 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532043300 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/712 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)c1) `ZINC001532043300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532043300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001532043300 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 20, 21, 31, 31, 31, 31, 31, 31, 14, 14, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 7, 20, 20, 21, 21, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/713 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)c1) `ZINC001532043300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532043300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001532043300 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 19, 20, 34, 34, 34, 34, 34, 34, 13, 13, 6, 6, 6, 6, 2, 6, 6, 3, 7, 7, 7, 19, 19, 20, 20, 34, 34, 34, 34, 34, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532043300 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 Building ZINC001532043300 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532043300 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 712) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)c1) `ZINC001532043300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532043300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001532043300 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 20, 21, 31, 31, 31, 31, 31, 31, 14, 14, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 7, 20, 20, 21, 21, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 713) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)c1) `ZINC001532043300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532043300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001532043300 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)cc2c2nc(CCOc3ccccc3)no2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 19, 20, 34, 34, 34, 34, 34, 34, 13, 13, 6, 6, 6, 6, 2, 6, 6, 3, 7, 7, 7, 19, 19, 20, 20, 34, 34, 34, 34, 34, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532043300 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532043300 Building ZINC001532054640 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532054640 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/714 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc(C)c(C(=O)OCC)s1) `ZINC001532054640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532054640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001532054640 none CCCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc(C)c(C(=O)OCC)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 23, 23, 24, 27, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/715 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc(C)c(C(=O)OCC)s1) `ZINC001532054640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532054640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001532054640 none CCCCCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc(C)c(C(=O)OCC)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 24, 24, 25, 30, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532054640 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 Building ZINC001532054640 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532054640 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 714) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc(C)c(C(=O)OCC)s1) `ZINC001532054640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532054640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001532054640 none CCCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc(C)c(C(=O)OCC)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 23, 23, 24, 27, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 715) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc(C)c(C(=O)OCC)s1) `ZINC001532054640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532054640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001532054640 none CCCCCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc(C)c(C(=O)OCC)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 24, 24, 25, 30, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532054640 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532054640 Building ZINC001532084076 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532084076 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/716 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(C)cc1Br) `ZINC001532084076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532084076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532084076 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(C)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 12, 36, 12, 12, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 12, 4, 5, 2, 5, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/717 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(C)cc1Br) `ZINC001532084076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532084076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532084076 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(C)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 13, 37, 13, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 13, 13, 13, 13, 13, 37, 37, 37, 13, 4, 5, 1, 5, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532084076 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 Building ZINC001532084076 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532084076 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 716) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(C)cc1Br) `ZINC001532084076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532084076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532084076 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(C)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 12, 36, 12, 12, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 12, 4, 5, 2, 5, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 717) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(C)cc1Br) `ZINC001532084076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532084076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532084076 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(C)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 13, 37, 13, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 13, 13, 13, 13, 13, 37, 37, 37, 13, 4, 5, 1, 5, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532084076 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532084076 Building ZINC001532088077 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532088077 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/718 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/718' -> `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)N1CCCSc2cc(Cl)ccc21) `ZINC001532088077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532088077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001532088077 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCSc2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 2, 10, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19] 42 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 64 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/719 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/719' -> `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)N1CCCSc2cc(Cl)ccc21) `ZINC001532088077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532088077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001532088077 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCSc2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 2, 11, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19] 38 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 60 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532088077 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 Building ZINC001532088077 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532088077 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 718) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCCSc2cc(Cl)ccc21) `ZINC001532088077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532088077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001532088077 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCSc2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 2, 10, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19] 42 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 64 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 719) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCCSc2cc(Cl)ccc21) `ZINC001532088077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532088077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001532088077 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCSc2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 2, 11, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19] 38 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 60 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532088077 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532088077 Building ZINC001532091008 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532091008 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/720 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001532091008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532091008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532091008 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 26, 26, 26, 26, 26, 26, 26, 2, 6, 6, 6, 10, 10, 10, 6, 6, 2, 2, 2, 2, 2, 2, 26, 26, 26, 2, 2, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/721 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001532091008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532091008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532091008 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 9, 28, 28, 28, 28, 28, 28, 28, 3, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 3, 3, 3, 28, 28, 28, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532091008 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 Building ZINC001532091008 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532091008 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 720) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001532091008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532091008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532091008 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 26, 26, 26, 26, 26, 26, 26, 2, 6, 6, 6, 10, 10, 10, 6, 6, 2, 2, 2, 2, 2, 2, 26, 26, 26, 2, 2, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 721) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001532091008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532091008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532091008 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 9, 28, 28, 28, 28, 28, 28, 28, 3, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 3, 3, 3, 28, 28, 28, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532091008 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091008 Building ZINC001532091009 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532091009 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/722 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001532091009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532091009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532091009 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 28, 28, 21, 28, 28, 28, 28, 2, 2, 2, 2, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 2, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/723 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001532091009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532091009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532091009 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 11, 27, 27, 23, 27, 27, 27, 27, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532091009 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 Building ZINC001532091009 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532091009 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 722) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001532091009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532091009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532091009 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 8, 28, 28, 21, 28, 28, 28, 28, 2, 2, 2, 2, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 2, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 723) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001532091009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532091009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532091009 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 11, 27, 27, 23, 27, 27, 27, 27, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532091009 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532091009 Building ZINC001532121291 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532121291 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/724 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532121291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532121291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532121291 none O=C(NCc1cccc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 35, 35, 35, 35, 35, 35, 35, 48, 48, 41, 48, 48, 32, 1, 1, 1, 4, 4, 4, 4, 4, 2, 14, 14, 35, 35, 35, 35, 35, 48, 48, 48, 48, 48, 35, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/725 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532121291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532121291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532121291 none O=C(NCc1cccc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 36, 36, 36, 36, 36, 36, 36, 48, 48, 45, 48, 48, 35, 1, 1, 1, 4, 4, 4, 4, 4, 2, 14, 14, 36, 36, 36, 36, 36, 48, 48, 48, 48, 48, 36, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532121291 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 Building ZINC001532121291 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532121291 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 724) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532121291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532121291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532121291 none O=C(NCc1cccc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 35, 35, 35, 35, 35, 35, 35, 48, 48, 41, 48, 48, 32, 1, 1, 1, 4, 4, 4, 4, 4, 2, 14, 14, 35, 35, 35, 35, 35, 48, 48, 48, 48, 48, 35, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 725) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532121291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532121291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532121291 none O=C(NCc1cccc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 14, 36, 36, 36, 36, 36, 36, 36, 48, 48, 45, 48, 48, 35, 1, 1, 1, 4, 4, 4, 4, 4, 2, 14, 14, 36, 36, 36, 36, 36, 48, 48, 48, 48, 48, 36, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532121291 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532121291 Building ZINC001532122345 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532122345 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/726 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)cc(Br)c2OC)cc1Cl) `ZINC001532122345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532122345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001532122345 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)cc(Br)c2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 17, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 4, 10, 10, 10, 10, 15, 6, 6, 6, 12, 12, 12, 6, 6, 4, 10, 10, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/727 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)cc(Br)c2OC)cc1Cl) `ZINC001532122345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532122345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001532122345 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)cc(Br)c2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 17, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 7, 10, 10, 10, 10, 15, 6, 6, 6, 12, 12, 12, 6, 6, 4, 10, 10, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532122345 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 Building ZINC001532122345 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532122345 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 726) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)cc(Br)c2OC)cc1Cl) `ZINC001532122345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532122345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001532122345 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)cc(Br)c2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 17, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 4, 10, 10, 10, 10, 15, 6, 6, 6, 12, 12, 12, 6, 6, 4, 10, 10, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 727) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)cc(Br)c2OC)cc1Cl) `ZINC001532122345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532122345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001532122345 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)cc(Br)c2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 17, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 7, 10, 10, 10, 10, 15, 6, 6, 6, 12, 12, 12, 6, 6, 4, 10, 10, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532122345 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532122345 Building ZINC001532129348 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532129348 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/728 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1) `ZINC001532129348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532129348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001532129348 none CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/729 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1) `ZINC001532129348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532129348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001532129348 none CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 3, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532129348 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 Building ZINC001532129348 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532129348 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 728) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1) `ZINC001532129348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532129348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001532129348 none CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 729) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1) `ZINC001532129348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532129348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001532129348 none CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 3, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532129348 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532129348 Building ZINC001532131501 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532131501 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/730 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1F) `ZINC001532131501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532131501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001532131501 none COc1ccc(N(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 9, 9, 9, 5, 4, 5, 18, 18, 18, 18, 18, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 19, 19, 19, 9, 9, 18, 18, 18, 18, 18, 4, 4, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/731 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1F) `ZINC001532131501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532131501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001532131501 none COc1ccc(N(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 8, 8, 5, 4, 5, 17, 18, 18, 18, 18, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 17, 17, 17, 8, 8, 17, 17, 18, 18, 18, 4, 4, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532131501 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 Building ZINC001532131501 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532131501 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 730) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1F) `ZINC001532131501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532131501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001532131501 none COc1ccc(N(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 9, 9, 9, 5, 4, 5, 18, 18, 18, 18, 18, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 19, 19, 19, 9, 9, 18, 18, 18, 18, 18, 4, 4, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 731) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1F) `ZINC001532131501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532131501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001532131501 none COc1ccc(N(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 8, 8, 5, 4, 5, 17, 18, 18, 18, 18, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 17, 17, 17, 8, 8, 17, 17, 18, 18, 18, 4, 4, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532131501 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532131501 Building ZINC001532170095 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532170095 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/732 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C) `ZINC001532170095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532170095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001532170095 none COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 13, 13, 13, 6, 6, 6, 2, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/733 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C) `ZINC001532170095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532170095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001532170095 none COc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 12, 12, 12, 6, 6, 6, 2, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532170095 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 Building ZINC001532170095 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532170095 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 732) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C) `ZINC001532170095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532170095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001532170095 none COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 13, 13, 13, 6, 6, 6, 2, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 733) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C) `ZINC001532170095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532170095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001532170095 none COc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 12, 12, 12, 6, 6, 6, 2, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532170095 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532170095 Building ZINC001532174328 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532174328 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/734 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)c2)c1) `ZINC001532174328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532174328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001532174328 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 45, 48, 48, 48, 48, 45, 25, 25, 25, 25, 25, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 25, 48, 48, 48, 48, 45, 48, 48, 48, 48, 25, 25, 25, 11, 11, 2, 3, 3, 25, 48] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/735 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)c2)c1) `ZINC001532174328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532174328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001532174328 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 45, 48, 48, 48, 48, 45, 25, 25, 25, 25, 25, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 25, 48, 48, 48, 48, 45, 48, 48, 48, 48, 25, 25, 25, 11, 11, 2, 3, 3, 25, 48] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532174328 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 Building ZINC001532174328 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532174328 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 734) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)c2)c1) `ZINC001532174328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532174328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001532174328 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 45, 48, 48, 48, 48, 45, 25, 25, 25, 25, 25, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 25, 48, 48, 48, 48, 45, 48, 48, 48, 48, 25, 25, 25, 11, 11, 2, 3, 3, 25, 48] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 735) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)c2)c1) `ZINC001532174328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532174328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001532174328 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 45, 48, 48, 48, 48, 45, 25, 25, 25, 25, 25, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 25, 48, 48, 48, 48, 45, 48, 48, 48, 48, 25, 25, 25, 11, 11, 2, 3, 3, 25, 48] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532174328 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532174328 Building ZINC001532194681 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532194681 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/736 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Cl)cc(Br)c21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532194681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532194681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001532194681 none O=C(N1CCc2cc(Cl)cc(Br)c21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 9, 9] 33 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/737 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Cl)cc(Br)c21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532194681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532194681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001532194681 none O=C(N1CCc2cc(Cl)cc(Br)c21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 9, 9] 33 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532194681 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 Building ZINC001532194681 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532194681 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 736) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Cl)cc(Br)c21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532194681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532194681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001532194681 none O=C(N1CCc2cc(Cl)cc(Br)c21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 9, 9] 33 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 737) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Cl)cc(Br)c21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532194681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532194681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001532194681 none O=C(N1CCc2cc(Cl)cc(Br)c21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 9, 9] 33 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532194681 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532194681 Building ZINC001532201522 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532201522 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/738 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c2ccccc2sc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532201522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532201522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001532201522 none CCOC(=O)c1c2ccccc2sc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 7, 27, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 38, 38, 38, 38, 38, 7, 7, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/739 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c2ccccc2sc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532201522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532201522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001532201522 none CCOC(=O)c1c2ccccc2sc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 5, 22, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 33, 33, 33, 33, 33, 5, 5, 5, 5, 1, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 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/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532201522 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 Building ZINC001532201522 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532201522 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 738) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c2ccccc2sc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532201522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532201522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001532201522 none CCOC(=O)c1c2ccccc2sc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 7, 27, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 38, 38, 38, 38, 38, 7, 7, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 739) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c2ccccc2sc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532201522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532201522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001532201522 none CCOC(=O)c1c2ccccc2sc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 5, 22, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 33, 33, 33, 33, 33, 5, 5, 5, 5, 1, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 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/150923/xbj-8058088.36/working/building/ZINC001532201522 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532201522 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532201522 Building ZINC001532234540 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532234540 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/740 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)s3)CCC2)cc1Cl) `ZINC001532234540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532234540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532234540 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)s3)CCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 14, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 27, 27, 27, 27, 27, 25, 25, 25, 4, 4, 4, 9, 9, 9, 4, 4, 2, 11, 11, 27, 27, 25, 25, 25, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/741 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)s3)CCC2)cc1Cl) `ZINC001532234540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532234540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532234540 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)s3)CCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 14, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 26, 27, 27, 27, 27, 27, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 2, 11, 11, 27, 27, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532234540 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 Building ZINC001532234540 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532234540 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 740) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)s3)CCC2)cc1Cl) `ZINC001532234540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532234540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532234540 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)s3)CCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 14, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 25, 27, 27, 27, 27, 27, 25, 25, 25, 4, 4, 4, 9, 9, 9, 4, 4, 2, 11, 11, 27, 27, 25, 25, 25, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 741) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)s3)CCC2)cc1Cl) `ZINC001532234540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532234540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532234540 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)s3)CCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 14, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 26, 27, 27, 27, 27, 27, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 2, 11, 11, 27, 27, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532234540 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532234540 Building ZINC001532288742 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532288742 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/742 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2cc(Br)cnc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532288742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532288742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001532288742 none O=C(Nc1cccc2cc(Br)cnc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 7, 27, 27, 27, 27, 27, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/743 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2cc(Br)cnc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532288742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532288742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001532288742 none O=C(Nc1cccc2cc(Br)cnc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 7, 27, 27, 27, 27, 27, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532288742 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 Building ZINC001532288742 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532288742 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 742) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2cc(Br)cnc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532288742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532288742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001532288742 none O=C(Nc1cccc2cc(Br)cnc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 7, 27, 27, 27, 27, 27, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 743) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2cc(Br)cnc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532288742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532288742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001532288742 none O=C(Nc1cccc2cc(Br)cnc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 12, 12, 12, 12, 12, 7, 27, 27, 27, 27, 27, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532288742 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532288742 Building ZINC001532314314 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532314314 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/744 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(C)nn1c1cc(C(F)(F)F)ccc1Cl) `ZINC001532314314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532314314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001532314314 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(C)nn1c1cc(C(F)(F)F)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 7, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 24, 50, 49, 50, 2, 2, 2, 2, 2, 2, 2, 7, 15, 15, 15, 15, 50, 26, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/745 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)nn1c1cc(C(F)(F)F)ccc1Cl) `ZINC001532314314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532314314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001532314314 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)nn1c1cc(C(F)(F)F)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 7, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 16, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 7, 15, 15, 15, 15, 50, 26, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532314314 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 Building ZINC001532314314 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532314314 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 744) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1cc(C)nn1c1cc(C(F)(F)F)ccc1Cl) `ZINC001532314314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532314314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001532314314 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(C)nn1c1cc(C(F)(F)F)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 7, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 24, 50, 49, 50, 2, 2, 2, 2, 2, 2, 2, 7, 15, 15, 15, 15, 50, 26, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 745) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1cc(C)nn1c1cc(C(F)(F)F)ccc1Cl) `ZINC001532314314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532314314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001532314314 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)nn1c1cc(C(F)(F)F)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 7, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 16, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 7, 15, 15, 15, 15, 50, 26, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532314314 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532314314 Building ZINC001532341360 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532341360 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/746 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl) `ZINC001532341360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532341360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532341360 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 27, 27, 27, 27, 5, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/747 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl) `ZINC001532341360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532341360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532341360 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 29, 29, 29, 29, 6, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532341360 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 Building ZINC001532341360 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532341360 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 746) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl) `ZINC001532341360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532341360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532341360 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 27, 27, 27, 27, 5, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 747) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl) `ZINC001532341360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532341360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532341360 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 29, 29, 29, 29, 6, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532341360 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341360 Building ZINC001532341361 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532341361 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/748 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl) `ZINC001532341361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532341361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532341361 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 27, 4, 1, 1, 1, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 44, 40, 43, 41, 24, 25, 26, 42] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 45]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/749 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl) `ZINC001532341361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532341361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532341361 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 27, 27, 27, 27, 6, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532341361 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 Building ZINC001532341361 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532341361 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 748) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl) `ZINC001532341361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532341361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532341361 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 27, 4, 1, 1, 1, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 44, 40, 43, 41, 24, 25, 26, 42] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 45]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 749) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl) `ZINC001532341361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532341361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532341361 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(OC(F)(F)F)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 27, 27, 27, 27, 6, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532341361 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532341361 Building ZINC001532358483 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532358483 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/750 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl) `ZINC001532358483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532358483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001532358483 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 6, 6, 6, 14, 14, 14, 6, 6, 3, 3, 3, 3, 3, 3, 21, 21, 3, 21, 3, 3, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/751 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl) `ZINC001532358483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532358483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001532358483 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 6, 6, 6, 11, 11, 11, 6, 6, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 3, 3, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532358483 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 Building ZINC001532358483 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532358483 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 750) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl) `ZINC001532358483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532358483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001532358483 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 6, 6, 6, 14, 14, 14, 6, 6, 3, 3, 3, 3, 3, 3, 21, 21, 3, 21, 3, 3, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 751) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl) `ZINC001532358483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532358483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001532358483 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 6, 6, 6, 11, 11, 11, 6, 6, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 3, 3, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532358483 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358483 Building ZINC001532358484 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532358484 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/752 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl) `ZINC001532358484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532358484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001532358484 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 6, 6, 6, 10, 10, 10, 6, 6, 3, 3, 3, 3, 3, 3, 22, 22, 4, 22, 3, 3, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/753 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl) `ZINC001532358484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532358484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001532358484 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 6, 6, 6, 14, 14, 14, 6, 6, 3, 3, 3, 3, 3, 3, 21, 21, 5, 21, 3, 3, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532358484 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 Building ZINC001532358484 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532358484 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 752) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl) `ZINC001532358484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532358484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001532358484 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 6, 6, 6, 10, 10, 10, 6, 6, 3, 3, 3, 3, 3, 3, 22, 22, 4, 22, 3, 3, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 753) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl) `ZINC001532358484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532358484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001532358484 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3cccc(C(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 6, 6, 6, 14, 14, 14, 6, 6, 3, 3, 3, 3, 3, 3, 21, 21, 5, 21, 3, 3, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532358484 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532358484 Building ZINC001532366516 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532366516 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/754 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(Br)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532366516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532366516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532366516 none CCOC(=O)c1cc(Br)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 35, 35, 10, 35, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 45, 45, 45, 45, 45, 10, 10, 10, 4, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/755 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(Br)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532366516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532366516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532366516 none CCOC(=O)c1cc(Br)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 10, 33, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 45, 45, 45, 45, 45, 10, 10, 10, 4, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532366516 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 Building ZINC001532366516 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532366516 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 754) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(Br)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532366516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532366516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532366516 none CCOC(=O)c1cc(Br)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 35, 35, 10, 35, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 45, 45, 45, 45, 45, 10, 10, 10, 4, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 755) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(Br)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532366516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532366516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532366516 none CCOC(=O)c1cc(Br)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 10, 33, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 45, 45, 45, 45, 45, 10, 10, 10, 4, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532366516 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532366516 Building ZINC001532431058 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532431058 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/756 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Br)ncc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532431058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532431058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001532431058 none O=C(Nc1c(Br)ncc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 6, 26, 26, 26, 26, 26, 11, 11] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/757 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Br)ncc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532431058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532431058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001532431058 none O=C(Nc1c(Br)ncc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 6, 26, 26, 26, 26, 26, 11, 11] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532431058 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 Building ZINC001532431058 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532431058 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 756) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Br)ncc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532431058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532431058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001532431058 none O=C(Nc1c(Br)ncc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 6, 26, 26, 26, 26, 26, 11, 11] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 757) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Br)ncc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532431058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532431058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001532431058 none O=C(Nc1c(Br)ncc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 6, 26, 26, 26, 26, 26, 11, 11] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532431058 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532431058 Building ZINC001532435294 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532435294 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/758 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(c1ccc(CNC(=O)OC(C)(C)C)cc1C)C1CC1) `ZINC001532435294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532435294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001532435294 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(c1ccc(CNC(=O)OC(C)(C)C)cc1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 5, 5, 4, 4, 16, 35, 49, 49, 50, 50, 50, 50, 5, 5, 5, 2, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/759 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(c1ccc(CNC(=O)OC(C)(C)C)cc1C)C1CC1) `ZINC001532435294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532435294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001532435294 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(c1ccc(CNC(=O)OC(C)(C)C)cc1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 6, 6, 4, 4, 23, 37, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532435294 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 Building ZINC001532435294 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532435294 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 758) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(c1ccc(CNC(=O)OC(C)(C)C)cc1C)C1CC1) `ZINC001532435294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532435294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001532435294 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(c1ccc(CNC(=O)OC(C)(C)C)cc1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 5, 5, 4, 4, 16, 35, 49, 49, 50, 50, 50, 50, 5, 5, 5, 2, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 759) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(c1ccc(CNC(=O)OC(C)(C)C)cc1C)C1CC1) `ZINC001532435294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532435294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001532435294 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(c1ccc(CNC(=O)OC(C)(C)C)cc1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 6, 6, 4, 4, 23, 37, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532435294 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532435294 Building ZINC001532446799 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001532446799 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/760 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 13, 1, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 3, 1, 3, 30, 30, 30, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/761 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 13, 1, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 3, 1, 3, 30, 30, 30, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/762 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/762' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 28, 28, 28, 28, 28, 13, 1, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 28, 3, 1, 3, 28, 28, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/763 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/763' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 28, 28, 28, 28, 28, 13, 1, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 28, 3, 1, 3, 28, 28, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532446799 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 Building ZINC001532446799 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001532446799 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 760) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 13, 1, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 3, 1, 3, 30, 30, 30, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 761) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 13, 1, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 3, 1, 3, 30, 30, 30, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 762) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 28, 28, 28, 28, 28, 13, 1, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 28, 3, 1, 3, 28, 28, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 763) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 28, 28, 28, 28, 28, 13, 1, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 28, 3, 1, 3, 28, 28, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532446799 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 Building ZINC001532446799 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001532446799 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 760) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 13, 1, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 3, 1, 3, 30, 30, 30, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 761) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 13, 1, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 3, 1, 3, 30, 30, 30, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 762) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 28, 28, 28, 28, 28, 13, 1, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 28, 3, 1, 3, 28, 28, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 763) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 28, 28, 28, 28, 28, 13, 1, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 28, 3, 1, 3, 28, 28, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532446799 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 Building ZINC001532446799 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001532446799 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 760) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 13, 1, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 3, 1, 3, 30, 30, 30, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 761) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 13, 1, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 3, 1, 3, 30, 30, 30, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 762) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 28, 28, 28, 28, 28, 13, 1, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 28, 3, 1, 3, 28, 28, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 763) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001532446799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001532446799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532446799 none Cc1c(Cl)cccc1N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 28, 28, 28, 28, 28, 13, 1, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 48, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 28, 3, 1, 3, 28, 28, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532446799 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532446799 Building ZINC001532509574 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532509574 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/764 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cncc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532509574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532509574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532509574 none O=C(N[C@H](c1cncc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 36, 36, 36, 36, 36, 36, 8, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 36, 36, 36, 12, 12, 12, 12, 12, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/765 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cncc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532509574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532509574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532509574 none O=C(N[C@H](c1cncc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 34, 34, 34, 34, 34, 34, 8, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 34, 34, 34, 12, 12, 12, 12, 12, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532509574 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 Building ZINC001532509574 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532509574 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 764) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cncc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532509574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532509574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532509574 none O=C(N[C@H](c1cncc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 36, 36, 36, 36, 36, 36, 8, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 36, 36, 36, 12, 12, 12, 12, 12, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 765) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cncc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532509574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532509574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532509574 none O=C(N[C@H](c1cncc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 34, 34, 34, 34, 34, 34, 8, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 34, 34, 34, 12, 12, 12, 12, 12, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532509574 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509574 Building ZINC001532509576 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532509576 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/766 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cncc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532509576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532509576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532509576 none O=C(N[C@@H](c1cncc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 35, 35, 35, 35, 35, 35, 8, 12, 12, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 35, 35, 35, 12, 12, 12, 12, 12, 4, 1, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/767 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cncc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532509576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532509576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532509576 none O=C(N[C@@H](c1cncc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 37, 37, 37, 37, 37, 37, 8, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 37, 37, 37, 14, 14, 14, 14, 14, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532509576 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 Building ZINC001532509576 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532509576 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 766) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cncc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532509576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532509576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532509576 none O=C(N[C@@H](c1cncc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 35, 35, 35, 35, 35, 35, 8, 12, 12, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 35, 35, 35, 12, 12, 12, 12, 12, 4, 1, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 767) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cncc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532509576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532509576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532509576 none O=C(N[C@@H](c1cncc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 37, 37, 37, 37, 37, 37, 8, 14, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 37, 37, 37, 14, 14, 14, 14, 14, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532509576 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532509576 Building ZINC001532526418 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532526418 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/768 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccc(F)c(F)c1) `ZINC001532526418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532526418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001532526418 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 18, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/769 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccc(F)c(F)c1) `ZINC001532526418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532526418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001532526418 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 22, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532526418 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 Building ZINC001532526418 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532526418 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 768) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccc(F)c(F)c1) `ZINC001532526418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532526418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001532526418 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 18, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 108 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 769) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccc(F)c(F)c1) `ZINC001532526418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532526418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001532526418 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 22, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532526418 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526418 Building ZINC001532526419 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532526419 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/770 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccc(F)c(F)c1) `ZINC001532526419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532526419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001532526419 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 22, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/771 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccc(F)c(F)c1) `ZINC001532526419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532526419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001532526419 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 18, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532526419 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 Building ZINC001532526419 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532526419 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 770) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccc(F)c(F)c1) `ZINC001532526419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532526419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001532526419 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 22, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 771) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccc(F)c(F)c1) `ZINC001532526419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532526419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001532526419 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 18, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532526419 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532526419 Building ZINC001532601821 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532601821 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/772 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)c(C(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532601821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532601821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532601821 none O=C(Nc1ccc(F)c(C(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 13, 39, 39, 39, 39, 39, 39, 39, 13, 1, 1, 1, 6, 6, 6, 6, 6, 3, 13, 13, 39, 39, 39, 39, 39, 13, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/773 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)c(C(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532601821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532601821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532601821 none O=C(Nc1ccc(F)c(C(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 13, 39, 39, 39, 39, 39, 39, 39, 13, 1, 1, 1, 6, 6, 6, 6, 6, 3, 13, 13, 39, 39, 39, 39, 39, 13, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532601821 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 Building ZINC001532601821 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532601821 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 772) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)c(C(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532601821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532601821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532601821 none O=C(Nc1ccc(F)c(C(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 13, 39, 39, 39, 39, 39, 39, 39, 13, 1, 1, 1, 6, 6, 6, 6, 6, 3, 13, 13, 39, 39, 39, 39, 39, 13, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 773) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)c(C(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532601821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532601821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001532601821 none O=C(Nc1ccc(F)c(C(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 13, 39, 39, 39, 39, 39, 39, 39, 13, 1, 1, 1, 6, 6, 6, 6, 6, 3, 13, 13, 39, 39, 39, 39, 39, 13, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532601821 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532601821 Building ZINC001532613710 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532613710 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/774 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@@H]1C) `ZINC001532613710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532613710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613710 none Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 14, 14, 17, 17, 14, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 16, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 7, 7, 19, 19, 19, 19, 19, 19, 19] 37 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/775 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@@H]1C) `ZINC001532613710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532613710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613710 none Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 20, 20, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 20, 9, 9, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 86 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532613710 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 Building ZINC001532613710 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532613710 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 774) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@@H]1C) `ZINC001532613710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532613710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613710 none Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 14, 14, 17, 17, 14, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 16, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 7, 7, 19, 19, 19, 19, 19, 19, 19] 37 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 775) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@@H]1C) `ZINC001532613710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532613710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613710 none Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 19, 20, 20, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 20, 9, 9, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 86 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532613710 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613710 Building ZINC001532613712 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532613712 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/776 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@H]1C) `ZINC001532613712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532613712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613712 none Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 20, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 20, 9, 9, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/777 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@H]1C) `ZINC001532613712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532613712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613712 none Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 13, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 15, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 7, 7, 17, 17, 17, 17, 17, 17, 17] 33 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 56 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532613712 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 Building ZINC001532613712 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532613712 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 776) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@H]1C) `ZINC001532613712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532613712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613712 none Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 20, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 20, 9, 9, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 777) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@H]1C) `ZINC001532613712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532613712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613712 none Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 13, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 15, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 7, 7, 17, 17, 17, 17, 17, 17, 17] 33 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 56 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532613712 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613712 Building ZINC001532613714 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532613714 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/778 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@@H]1C) `ZINC001532613714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532613714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613714 none Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 11, 17, 17, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 17, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 17, 17, 5, 5, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/779 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@@H]1C) `ZINC001532613714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532613714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613714 none Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 16, 16, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 35, 35, 35, 35, 35, 35, 35, 16, 16, 16, 16, 16, 16, 5, 5, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532613714 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 Building ZINC001532613714 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532613714 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 778) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@@H]1C) `ZINC001532613714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532613714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613714 none Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 11, 17, 17, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 17, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 17, 17, 5, 5, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 779) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@@H]1C) `ZINC001532613714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532613714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613714 none Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 16, 16, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 35, 35, 35, 35, 35, 35, 35, 16, 16, 16, 16, 16, 16, 5, 5, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532613714 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613714 Building ZINC001532613716 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532613716 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/780 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@H]1C) `ZINC001532613716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532613716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613716 none Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 16, 18, 18, 18, 14, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 34, 34, 34, 34, 34, 34, 34, 18, 18, 18, 18, 18, 18, 5, 5, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/781 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@H]1C) `ZINC001532613716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532613716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613716 none Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 15, 17, 17, 17, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 17, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 17, 17, 5, 5, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532613716 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 Building ZINC001532613716 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532613716 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 780) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@H]1C) `ZINC001532613716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532613716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613716 none Cc1cc(Cl)ccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 16, 18, 18, 18, 14, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 34, 34, 34, 34, 34, 34, 34, 18, 18, 18, 18, 18, 18, 5, 5, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 781) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@H]1C) `ZINC001532613716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532613716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001532613716 none Cc1cc(Cl)ccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 15, 17, 17, 17, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 17, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 17, 17, 5, 5, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532613716 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532613716 Building ZINC001532641160 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532641160 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/782 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)c1) `ZINC001532641160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532641160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532641160 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 8, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 6, 6, 6, 6, 2, 6, 6, 2, 24, 24, 24, 4, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/783 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)c1) `ZINC001532641160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532641160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532641160 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 8, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 6, 6, 6, 6, 6, 6, 6, 2, 24, 24, 24, 4, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532641160 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 Building ZINC001532641160 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532641160 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 782) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)c1) `ZINC001532641160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532641160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532641160 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 8, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 6, 6, 6, 6, 2, 6, 6, 2, 24, 24, 24, 4, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 783) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)c1) `ZINC001532641160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532641160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532641160 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3c[nH]c4ncc(Br)cc34)cs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 8, 1, 1, 17, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 6, 6, 6, 6, 6, 6, 6, 2, 24, 24, 24, 4, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532641160 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532641160 Building ZINC001532748551 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532748551 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/784 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCSc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532748551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532748551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532748551 none O=C(N[C@@H]1CCCSc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/785 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCSc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532748551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532748551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532748551 none O=C(N[C@@H]1CCCSc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532748551 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 Building ZINC001532748551 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532748551 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 784) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCSc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532748551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532748551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532748551 none O=C(N[C@@H]1CCCSc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 785) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCSc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532748551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532748551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532748551 none O=C(N[C@@H]1CCCSc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532748551 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748551 Building ZINC001532748553 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532748553 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/786 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCSc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532748553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532748553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532748553 none O=C(N[C@H]1CCCSc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/787 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCSc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532748553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532748553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532748553 none O=C(N[C@H]1CCCSc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532748553 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 Building ZINC001532748553 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532748553 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 786) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCSc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532748553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532748553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532748553 none O=C(N[C@H]1CCCSc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 787) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCSc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532748553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532748553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001532748553 none O=C(N[C@H]1CCCSc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532748553 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532748553 Building ZINC001532758572 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532758572 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/788 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(c2ccc(F)cc2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532758572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532758572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001532758572 none O=C(Nc1c(c2ccc(F)cc2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 23, 23, 35, 35, 34, 35, 35, 35, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 14, 35, 35, 35, 35, 23, 23, 23, 23, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/789 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(c2ccc(F)cc2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532758572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532758572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001532758572 none O=C(Nc1c(c2ccc(F)cc2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 23, 23, 35, 35, 34, 35, 35, 35, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 14, 35, 35, 35, 35, 23, 23, 23, 23, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532758572 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 Building ZINC001532758572 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532758572 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 788) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(c2ccc(F)cc2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532758572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532758572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001532758572 none O=C(Nc1c(c2ccc(F)cc2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 23, 23, 35, 35, 34, 35, 35, 35, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 14, 35, 35, 35, 35, 23, 23, 23, 23, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 789) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(c2ccc(F)cc2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532758572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532758572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001532758572 none O=C(Nc1c(c2ccc(F)cc2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 23, 23, 35, 35, 34, 35, 35, 35, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 14, 35, 35, 35, 35, 23, 23, 23, 23, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532758572 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532758572 Building ZINC001532828225 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532828225 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/790 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532828225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532828225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001532828225 none CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 17, 18, 18, 17, 18, 18, 18, 18, 18, 18, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 16, 16, 16, 16, 16, 17, 17, 18, 18, 17, 18, 2, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/791 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532828225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532828225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001532828225 none CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 10, 10, 10, 10, 10, 12, 12, 17, 17, 17, 17, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 123 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532828225 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 Building ZINC001532828225 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532828225 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 790) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532828225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532828225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001532828225 none CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 17, 18, 18, 17, 18, 18, 18, 18, 18, 18, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 16, 16, 16, 16, 16, 17, 17, 18, 18, 17, 18, 2, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 791) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532828225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532828225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001532828225 none CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 10, 10, 10, 10, 10, 12, 12, 17, 17, 17, 17, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 123 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532828225 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828225 Building ZINC001532828226 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532828226 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/792 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532828226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532828226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001532828226 none CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 12, 17, 17, 12, 17, 17, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 10, 10, 10, 10, 10, 12, 12, 17, 17, 12, 17, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/793 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532828226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532828226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001532828226 none CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 2, 8, 8, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 13, 13, 13, 13, 13, 15, 15, 17, 17, 17, 17, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532828226 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 Building ZINC001532828226 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532828226 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 792) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532828226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532828226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001532828226 none CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 12, 17, 17, 12, 17, 17, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 10, 10, 10, 10, 10, 12, 12, 17, 17, 12, 17, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 793) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001532828226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532828226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001532828226 none CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 2, 8, 8, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 13, 13, 13, 13, 13, 15, 15, 17, 17, 17, 17, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532828226 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532828226 Building ZINC001532837124 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532837124 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/794 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532837124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532837124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532837124 none CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 4, 9, 9, 17, 19, 19, 17, 19, 19, 19, 19, 19, 19, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 17, 17, 19, 19, 17, 19, 4, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/795 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532837124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532837124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532837124 none CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 3, 9, 9, 18, 20, 20, 18, 20, 20, 20, 20, 20, 20, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 18, 18, 20, 20, 18, 20, 3, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532837124 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 Building ZINC001532837124 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532837124 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 794) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532837124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532837124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532837124 none CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 4, 9, 9, 17, 19, 19, 17, 19, 19, 19, 19, 19, 19, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 17, 17, 19, 19, 17, 19, 4, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 795) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532837124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532837124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532837124 none CC[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 3, 9, 9, 18, 20, 20, 18, 20, 20, 20, 20, 20, 20, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 18, 18, 20, 20, 18, 20, 3, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532837124 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837124 Building ZINC001532837127 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532837127 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/796 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532837127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532837127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532837127 none CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 3, 10, 10, 19, 21, 21, 19, 21, 21, 21, 21, 21, 21, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 19, 19, 21, 21, 19, 21, 3, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/797 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532837127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532837127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532837127 none CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 4, 10, 10, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 18, 18, 20, 20, 20, 20, 4, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532837127 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 Building ZINC001532837127 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532837127 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 796) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532837127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532837127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532837127 none CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 3, 10, 10, 19, 21, 21, 19, 21, 21, 21, 21, 21, 21, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 19, 19, 21, 21, 19, 21, 3, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 797) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001532837127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532837127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001532837127 none CC[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 4, 10, 10, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 18, 18, 20, 20, 20, 20, 4, 12, 12] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532837127 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532837127 Building ZINC001532888663 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532888663 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/798 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CC1(CCOCC1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532888663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532888663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001532888663 none O=C(Nc1nc2c(s1)CC1(CCOCC1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 18, 20, 10, 34, 34, 34, 34, 34, 34, 34, 34, 27, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 1, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/799 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CC1(CCOCC1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532888663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532888663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001532888663 none O=C(Nc1nc2c(s1)CC1(CCOCC1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 17, 19, 9, 34, 34, 34, 34, 34, 34, 34, 34, 27, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 2, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532888663 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 Building ZINC001532888663 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532888663 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 798) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CC1(CCOCC1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532888663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532888663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001532888663 none O=C(Nc1nc2c(s1)CC1(CCOCC1)CC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 18, 20, 10, 34, 34, 34, 34, 34, 34, 34, 34, 27, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 1, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 799) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(s1)CC1(CCOCC1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532888663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532888663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001532888663 none O=C(Nc1nc2c(s1)CC1(CCOCC1)CC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 14, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 17, 19, 9, 34, 34, 34, 34, 34, 34, 34, 34, 27, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 2, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532888663 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532888663 Building ZINC001532934210 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532934210 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/800 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532934210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532934210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001532934210 none CC(C)(C)OC(=O)[C@H]1c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 6, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/801 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532934210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532934210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001532934210 none CC(C)(C)OC(=O)[C@H]1c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 9, 37, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532934210 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 Building ZINC001532934210 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532934210 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 800) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532934210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532934210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001532934210 none CC(C)(C)OC(=O)[C@H]1c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 6, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 801) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532934210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532934210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001532934210 none CC(C)(C)OC(=O)[C@H]1c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 9, 37, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532934210 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934210 Building ZINC001532934211 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532934211 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/802 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532934211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532934211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001532934211 none CC(C)(C)OC(=O)[C@@H]1c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 9, 37, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/803 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532934211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532934211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001532934211 none CC(C)(C)OC(=O)[C@@H]1c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 6, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532934211 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 Building ZINC001532934211 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532934211 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 802) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532934211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532934211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001532934211 none CC(C)(C)OC(=O)[C@@H]1c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 9, 37, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 803) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001532934211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532934211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001532934211 none CC(C)(C)OC(=O)[C@@H]1c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 6, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532934211 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532934211 Building ZINC001532954255 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532954255 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/804 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532954255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532954255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001532954255 none O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 25, 25, 25, 25, 6, 6, 6, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/805 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532954255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532954255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001532954255 none O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 25, 25, 25, 25, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532954255 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 Building ZINC001532954255 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001532954255 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 804) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532954255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001532954255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001532954255 none O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 25, 25, 25, 25, 6, 6, 6, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 805) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001532954255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001532954255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001532954255 none O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 25, 25, 25, 25, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001532954255 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001532954255 Building ZINC001533015891 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533015891 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/806 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1) `ZINC001533015891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533015891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533015891 none Cc1cccc(C)c1OC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 15, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 4, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 2, 6, 6, 6, 6, 6, 6, 6, 7, 7, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/807 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1) `ZINC001533015891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533015891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533015891 none Cc1cccc(C)c1OC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 19, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 19, 3, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533015891 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 Building ZINC001533015891 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533015891 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 806) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1) `ZINC001533015891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533015891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533015891 none Cc1cccc(C)c1OC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 15, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 4, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 2, 6, 6, 6, 6, 6, 6, 6, 7, 7, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 807) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1) `ZINC001533015891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533015891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533015891 none Cc1cccc(C)c1OC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 19, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 19, 3, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533015891 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015891 Building ZINC001533015892 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533015892 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/808 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1) `ZINC001533015892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533015892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533015892 none Cc1cccc(C)c1OC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 17, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 4, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 2, 6, 6, 6, 6, 6, 6, 6, 7, 7, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 103 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/809 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1) `ZINC001533015892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533015892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533015892 none Cc1cccc(C)c1OC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 16, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 4, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 7, 7, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 103 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533015892 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 Building ZINC001533015892 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533015892 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 808) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1) `ZINC001533015892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533015892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533015892 none Cc1cccc(C)c1OC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 17, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 4, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 2, 6, 6, 6, 6, 6, 6, 6, 7, 7, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 103 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 809) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1) `ZINC001533015892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533015892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533015892 none Cc1cccc(C)c1OC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 16, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 4, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 7, 7, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 103 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533015892 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533015892 Building ZINC001533020829 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533020829 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/810 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(Cl)ccc(Br)c2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001533020829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533020829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533020829 none O=C(Nc1ccc2c(Cl)ccc(Br)c2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/811 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(Cl)ccc(Br)c2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001533020829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533020829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533020829 none O=C(Nc1ccc2c(Cl)ccc(Br)c2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533020829 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 Building ZINC001533020829 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533020829 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 810) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(Cl)ccc(Br)c2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001533020829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533020829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533020829 none O=C(Nc1ccc2c(Cl)ccc(Br)c2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 811) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(Cl)ccc(Br)c2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001533020829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533020829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533020829 none O=C(Nc1ccc2c(Cl)ccc(Br)c2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533020829 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533020829 Building ZINC001533046174 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533046174 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/812 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1) `ZINC001533046174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533046174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001533046174 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 12, 29, 29, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 22, 22, 8, 22, 22, 22, 29, 29, 41, 29, 43, 43, 43, 29, 29, 4, 3, 3, 3, 3, 3, 3, 22, 22, 8, 22, 41, 41, 41, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 231 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/813 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1) `ZINC001533046174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533046174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001533046174 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 30, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 21, 21, 8, 21, 21, 21, 30, 30, 40, 30, 45, 45, 45, 30, 30, 4, 3, 3, 3, 3, 3, 3, 21, 21, 8, 21, 40, 40, 40, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533046174 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 Building ZINC001533046174 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533046174 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 812) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1) `ZINC001533046174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533046174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001533046174 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 12, 29, 29, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 22, 22, 8, 22, 22, 22, 29, 29, 41, 29, 43, 43, 43, 29, 29, 4, 3, 3, 3, 3, 3, 3, 22, 22, 8, 22, 41, 41, 41, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 231 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 813) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1) `ZINC001533046174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533046174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001533046174 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 30, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 21, 21, 8, 21, 21, 21, 30, 30, 40, 30, 45, 45, 45, 30, 30, 4, 3, 3, 3, 3, 3, 3, 21, 21, 8, 21, 40, 40, 40, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533046174 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046174 Building ZINC001533046175 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533046175 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/814 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1) `ZINC001533046175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533046175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001533046175 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 30, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 22, 22, 8, 22, 22, 22, 30, 30, 39, 30, 45, 45, 45, 30, 30, 4, 3, 3, 3, 3, 3, 3, 22, 22, 11, 22, 39, 39, 39, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 242 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/815 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1) `ZINC001533046175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533046175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001533046175 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 12, 30, 30, 8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 8, 22, 22, 22, 30, 30, 42, 30, 44, 44, 44, 30, 30, 4, 2, 2, 2, 2, 2, 2, 22, 22, 8, 22, 42, 42, 42, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533046175 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 Building ZINC001533046175 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533046175 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 814) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1) `ZINC001533046175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533046175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001533046175 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 30, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 22, 22, 8, 22, 22, 22, 30, 30, 39, 30, 45, 45, 45, 30, 30, 4, 3, 3, 3, 3, 3, 3, 22, 22, 11, 22, 39, 39, 39, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 242 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 815) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1) `ZINC001533046175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533046175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001533046175 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccccc2Cl)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 12, 30, 30, 8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 8, 22, 22, 22, 30, 30, 42, 30, 44, 44, 44, 30, 30, 4, 2, 2, 2, 2, 2, 2, 22, 22, 8, 22, 42, 42, 42, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 233 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533046175 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533046175 Building ZINC001533131496 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533131496 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/816 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(F)cc1F)C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533131496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533131496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533131496 none O=C(N(Cc1ccc(F)cc1F)C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 17, 24, 24, 21, 24, 24, 24, 24, 8, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/817 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(F)cc1F)C1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533131496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533131496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533131496 none O=C(N(Cc1ccc(F)cc1F)C1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 16, 25, 25, 20, 25, 25, 25, 25, 8, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533131496 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 Building ZINC001533131496 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533131496 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 816) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(F)cc1F)C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533131496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533131496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533131496 none O=C(N(Cc1ccc(F)cc1F)C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 17, 24, 24, 21, 24, 24, 24, 24, 8, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 817) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(F)cc1F)C1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533131496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533131496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533131496 none O=C(N(Cc1ccc(F)cc1F)C1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 16, 25, 25, 20, 25, 25, 25, 25, 8, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533131496 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533131496 Building ZINC001533132029 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533132029 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/818 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C(C)C)cc1Cl) `ZINC001533132029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533132029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001533132029 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 17, 17, 17, 13, 17, 17, 17, 4, 6, 6, 6, 6, 6, 8, 8, 8, 6, 6, 9, 9, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/819 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C(C)C)cc1Cl) `ZINC001533132029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533132029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001533132029 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 5, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 17, 17, 17, 13, 17, 17, 17, 4, 6, 6, 6, 6, 6, 8, 8, 8, 6, 6, 10, 10, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533132029 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 Building ZINC001533132029 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533132029 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 818) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C(C)C)cc1Cl) `ZINC001533132029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533132029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001533132029 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 17, 17, 17, 13, 17, 17, 17, 4, 6, 6, 6, 6, 6, 8, 8, 8, 6, 6, 9, 9, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 819) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C(C)C)cc1Cl) `ZINC001533132029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533132029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001533132029 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 5, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 17, 17, 17, 13, 17, 17, 17, 4, 6, 6, 6, 6, 6, 8, 8, 8, 6, 6, 10, 10, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533132029 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533132029 Building ZINC001533133997 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533133997 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/820 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@@H]2c2ccc(Cl)cc2)cn1) `ZINC001533133997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533133997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001533133997 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@@H]2c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 10, 10, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 11, 18, 18, 18, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/821 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@@H]2c2ccc(Cl)cc2)cn1) `ZINC001533133997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533133997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001533133997 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@@H]2c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 11, 11, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 17, 17, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533133997 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 Building ZINC001533133997 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533133997 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 820) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@@H]2c2ccc(Cl)cc2)cn1) `ZINC001533133997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533133997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001533133997 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@@H]2c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 10, 10, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 11, 18, 18, 18, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 821) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@@H]2c2ccc(Cl)cc2)cn1) `ZINC001533133997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533133997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001533133997 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@@H]2c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 11, 11, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 17, 17, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533133997 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533133997 Building ZINC001533134002 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533134002 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/822 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@H]2c2ccc(Cl)cc2)cn1) `ZINC001533134002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533134002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001533134002 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@H]2c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 19, 10, 10, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/823 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@H]2c2ccc(Cl)cc2)cn1) `ZINC001533134002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533134002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001533134002 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@H]2c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 11, 11, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 11] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533134002 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 Building ZINC001533134002 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533134002 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 822) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@H]2c2ccc(Cl)cc2)cn1) `ZINC001533134002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533134002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001533134002 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@H]2c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 19, 10, 10, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 823) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@H]2c2ccc(Cl)cc2)cn1) `ZINC001533134002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533134002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001533134002 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3sccc3[C@H]2c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 11, 11, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 11] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533134002 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533134002 Building ZINC001533185773 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533185773 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/824 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccc(c2cccnc2)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533185773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533185773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533185773 none O=C(N(Cc1cccc(c2cccnc2)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 10, 22, 22, 22, 22, 22, 34, 34, 34, 34, 34, 22, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 22, 22, 22, 34, 34, 34, 34, 22, 6, 6, 6, 6, 6, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/825 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccc(c2cccnc2)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533185773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533185773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533185773 none O=C(N(Cc1cccc(c2cccnc2)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 11, 22, 22, 22, 22, 22, 37, 37, 37, 37, 37, 22, 6, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 22, 22, 22, 37, 37, 37, 37, 22, 6, 6, 6, 6, 6, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533185773 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 Building ZINC001533185773 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533185773 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 824) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccc(c2cccnc2)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533185773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533185773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533185773 none O=C(N(Cc1cccc(c2cccnc2)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 10, 22, 22, 22, 22, 22, 34, 34, 34, 34, 34, 22, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 22, 22, 22, 34, 34, 34, 34, 22, 6, 6, 6, 6, 6, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 825) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccc(c2cccnc2)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533185773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533185773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533185773 none O=C(N(Cc1cccc(c2cccnc2)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 11, 22, 22, 22, 22, 22, 37, 37, 37, 37, 37, 22, 6, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 22, 22, 22, 37, 37, 37, 37, 22, 6, 6, 6, 6, 6, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533185773 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533185773 Building ZINC001533281368 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533281368 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/826 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533281368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533281368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533281368 none CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 32, 13, 32, 13, 13, 5, 13, 13, 13, 13, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 13, 13, 17, 17, 17, 3, 3, 1, 3] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/827 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533281368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533281368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533281368 none CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 13, 33, 13, 13, 5, 13, 13, 13, 13, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 13, 13, 17, 17, 17, 3, 3, 1, 3] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533281368 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 Building ZINC001533281368 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533281368 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 826) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533281368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533281368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533281368 none CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 32, 13, 32, 13, 13, 5, 13, 13, 13, 13, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 13, 13, 17, 17, 17, 3, 3, 1, 3] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 827) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533281368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533281368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533281368 none CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 13, 33, 13, 13, 5, 13, 13, 13, 13, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 13, 13, 17, 17, 17, 3, 3, 1, 3] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533281368 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533281368 Building ZINC001533307443 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533307443 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/828 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533307443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533307443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001533307443 none CC(C)(Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 22, 40, 40, 40, 40, 40, 40, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 22, 22, 40, 40, 40, 40, 4, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/829 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533307443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533307443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001533307443 none CC(C)(Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 23, 40, 40, 40, 40, 40, 40, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 23, 23, 40, 40, 40, 40, 4, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533307443 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 Building ZINC001533307443 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533307443 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 828) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533307443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533307443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001533307443 none CC(C)(Cc1cccc(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 22, 40, 40, 40, 40, 40, 40, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 22, 22, 40, 40, 40, 40, 4, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 829) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533307443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533307443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001533307443 none CC(C)(Cc1cccc(Br)c1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 23, 40, 40, 40, 40, 40, 40, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 23, 23, 40, 40, 40, 40, 4, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533307443 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533307443 Building ZINC001533349525 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533349525 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/830 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C) `ZINC001533349525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533349525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533349525 none CC(C)(C)OC(=O)N1c2ccccc2[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 22, 10, 22, 10, 10, 10, 10, 10, 10, 10, 6, 10, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/831 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C) `ZINC001533349525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533349525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533349525 none CC(C)(C)OC(=O)N1c2ccccc2[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 22, 9, 22, 9, 9, 9, 9, 9, 9, 9, 5, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533349525 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 Building ZINC001533349525 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533349525 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 830) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C) `ZINC001533349525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533349525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533349525 none CC(C)(C)OC(=O)N1c2ccccc2[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 22, 10, 22, 10, 10, 10, 10, 10, 10, 10, 6, 10, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 831) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C) `ZINC001533349525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533349525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533349525 none CC(C)(C)OC(=O)N1c2ccccc2[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 22, 9, 22, 9, 9, 9, 9, 9, 9, 9, 5, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533349525 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349525 Building ZINC001533349529 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533349529 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/832 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C) `ZINC001533349529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533349529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533349529 none CC(C)(C)OC(=O)N1c2ccccc2[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 22, 14, 22, 14, 14, 14, 14, 14, 14, 14, 9, 14, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/833 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C) `ZINC001533349529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533349529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533349529 none CC(C)(C)OC(=O)N1c2ccccc2[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 18, 17, 18, 17, 17, 17, 17, 17, 17, 17, 8, 17, 5, 1, 5, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 17, 17, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533349529 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 Building ZINC001533349529 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533349529 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 832) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C) `ZINC001533349529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533349529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533349529 none CC(C)(C)OC(=O)N1c2ccccc2[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 22, 14, 22, 14, 14, 14, 14, 14, 14, 14, 9, 14, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 833) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C) `ZINC001533349529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533349529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533349529 none CC(C)(C)OC(=O)N1c2ccccc2[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 18, 17, 18, 17, 17, 17, 17, 17, 17, 17, 8, 17, 5, 1, 5, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 17, 17, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533349529 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533349529 Building ZINC001533356816 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533356816 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/834 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc3c(c2)OCCO3)CCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533356816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533356816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001533356816 none O=C(NCC1(c2ccc3c(c2)OCCO3)CCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 32, 48, 48, 48, 48, 48, 48, 48, 48, 48, 32, 32, 32, 32, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 48, 48, 48, 48, 48, 48, 48, 32, 32, 32, 32, 32, 32, 32, 32, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/835 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc3c(c2)OCCO3)CCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533356816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533356816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001533356816 none O=C(NCC1(c2ccc3c(c2)OCCO3)CCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 17, 33, 48, 49, 49, 49, 48, 49, 49, 49, 49, 33, 33, 33, 33, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 49, 49, 49, 49, 49, 49, 49, 33, 33, 33, 33, 33, 33, 33, 33, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533356816 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 Building ZINC001533356816 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533356816 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 834) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc3c(c2)OCCO3)CCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533356816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533356816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001533356816 none O=C(NCC1(c2ccc3c(c2)OCCO3)CCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 32, 48, 48, 48, 48, 48, 48, 48, 48, 48, 32, 32, 32, 32, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 48, 48, 48, 48, 48, 48, 48, 32, 32, 32, 32, 32, 32, 32, 32, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 835) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc3c(c2)OCCO3)CCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533356816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533356816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001533356816 none O=C(NCC1(c2ccc3c(c2)OCCO3)CCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 17, 33, 48, 49, 49, 49, 48, 49, 49, 49, 49, 33, 33, 33, 33, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 49, 49, 49, 49, 49, 49, 49, 33, 33, 33, 33, 33, 33, 33, 33, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533356816 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533356816 Building ZINC001533385813 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533385813 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/836 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3c(c2)OCCO3)s1) `ZINC001533385813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533385813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001533385813 none Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3c(c2)OCCO3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 16, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 27, 27, 27, 27, 27, 27, 16, 16, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/837 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3c(c2)OCCO3)s1) `ZINC001533385813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533385813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001533385813 none Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3c(c2)OCCO3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 18, 7, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 18, 18, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533385813 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 Building ZINC001533385813 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533385813 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 836) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3c(c2)OCCO3)s1) `ZINC001533385813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533385813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001533385813 none Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3c(c2)OCCO3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 16, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 27, 27, 27, 27, 27, 27, 16, 16, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 837) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3c(c2)OCCO3)s1) `ZINC001533385813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533385813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001533385813 none Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3c(c2)OCCO3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 18, 7, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 18, 18, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533385813 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533385813 Building ZINC001533478824 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533478824 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/838 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001533478824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533478824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001533478824 none CC[C@@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 7, 22, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 22, 26, 26, 22, 26, 26, 26, 26, 26, 26, 26, 4, 7, 7, 26, 26, 22, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/839 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001533478824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533478824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001533478824 none CC[C@@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 8, 23, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 23, 26, 26, 23, 26, 26, 28, 28, 28, 28, 28, 4, 8, 8, 26, 26, 23, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533478824 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 Building ZINC001533478824 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533478824 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 838) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001533478824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533478824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001533478824 none CC[C@@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 7, 22, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 22, 26, 26, 22, 26, 26, 26, 26, 26, 26, 26, 4, 7, 7, 26, 26, 22, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 839) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001533478824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533478824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001533478824 none CC[C@@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 8, 23, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 23, 26, 26, 23, 26, 26, 28, 28, 28, 28, 28, 4, 8, 8, 26, 26, 23, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533478824 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478824 Building ZINC001533478876 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533478876 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/840 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001533478876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533478876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001533478876 none CC[C@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 8, 23, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 23, 26, 26, 23, 26, 26, 28, 28, 28, 28, 28, 4, 8, 8, 26, 26, 23, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/841 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001533478876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533478876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001533478876 none CC[C@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 21, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 21, 25, 25, 21, 25, 25, 25, 25, 25, 25, 25, 4, 7, 7, 25, 25, 21, 25, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533478876 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 Building ZINC001533478876 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533478876 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 840) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001533478876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533478876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001533478876 none CC[C@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 8, 23, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 23, 26, 26, 23, 26, 26, 28, 28, 28, 28, 28, 4, 8, 8, 26, 26, 23, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 841) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001533478876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533478876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001533478876 none CC[C@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 21, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 21, 25, 25, 21, 25, 25, 25, 25, 25, 25, 25, 4, 7, 7, 25, 25, 21, 25, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533478876 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533478876 Building ZINC001533514136 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533514136 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/842 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(c3cccc(F)c3)s2)CC1) `ZINC001533514136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533514136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533514136 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(c3cccc(F)c3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 4, 4, 4, 4, 10, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 16, 16, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 34, 35, 4, 5, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/843 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(c3cccc(F)c3)s2)CC1) `ZINC001533514136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533514136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533514136 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(c3cccc(F)c3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 4, 4, 4, 4, 10, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 15, 15, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 34, 35, 4, 5, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533514136 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 Building ZINC001533514136 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533514136 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 842) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(c3cccc(F)c3)s2)CC1) `ZINC001533514136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533514136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533514136 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(c3cccc(F)c3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 4, 4, 4, 4, 10, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 16, 16, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 34, 35, 4, 5, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 843) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(c3cccc(F)c3)s2)CC1) `ZINC001533514136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533514136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533514136 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccc(c3cccc(F)c3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 4, 4, 4, 4, 10, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 15, 15, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 34, 35, 4, 5, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533514136 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533514136 Building ZINC001533530370 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533530370 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/844 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(F)cc(Br)cc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533530370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533530370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001533530370 none O=C(N1CCc2c(F)cc(Br)cc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 15, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 45 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/845 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(F)cc(Br)cc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533530370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533530370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001533530370 none O=C(N1CCc2c(F)cc(Br)cc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 15, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 47 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533530370 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 Building ZINC001533530370 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533530370 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 844) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(F)cc(Br)cc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533530370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533530370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001533530370 none O=C(N1CCc2c(F)cc(Br)cc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 15, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 45 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 845) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(F)cc(Br)cc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533530370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533530370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001533530370 none O=C(N1CCc2c(F)cc(Br)cc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 15, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 47 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533530370 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533530370 Building ZINC001533667515 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533667515 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/846 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/847 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 34, 34, 35, 35, 34, 35, 35, 35, 40, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/848 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/848' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/849 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/849' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 34, 34, 35, 35, 34, 35, 35, 35, 40, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533667515 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 Building ZINC001533667515 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533667515 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 846) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 847) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 34, 34, 35, 35, 34, 35, 35, 35, 40, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 848) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 849) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 34, 34, 35, 35, 34, 35, 35, 35, 40, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533667515 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 Building ZINC001533667515 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533667515 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 846) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 847) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 34, 34, 35, 35, 34, 35, 35, 35, 40, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 848) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 849) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 34, 34, 35, 35, 34, 35, 35, 35, 40, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533667515 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 Building ZINC001533667515 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533667515 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 846) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 847) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 34, 34, 35, 35, 34, 35, 35, 35, 40, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 848) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 849) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667515.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533667515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667515 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 34, 34, 35, 35, 34, 35, 35, 35, 40, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533667515 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667515 Building ZINC001533667516 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533667516 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/850 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 18, 35, 35, 35, 35, 35, 35, 35, 35, 41, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/851 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 3, 3, 15, 27, 27, 30, 30, 27, 30, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/852 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/852' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 18, 35, 35, 35, 35, 35, 35, 35, 35, 41, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/853 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/853' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 3, 3, 15, 27, 27, 30, 30, 27, 30, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533667516 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 Building ZINC001533667516 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533667516 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 850) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 18, 35, 35, 35, 35, 35, 35, 35, 35, 41, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 851) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 3, 3, 15, 27, 27, 30, 30, 27, 30, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 852) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 18, 35, 35, 35, 35, 35, 35, 35, 35, 41, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 853) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 3, 3, 15, 27, 27, 30, 30, 27, 30, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533667516 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 Building ZINC001533667516 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533667516 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 850) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 18, 35, 35, 35, 35, 35, 35, 35, 35, 41, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 851) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 3, 3, 15, 27, 27, 30, 30, 27, 30, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 852) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 18, 35, 35, 35, 35, 35, 35, 35, 35, 41, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 853) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 3, 3, 15, 27, 27, 30, 30, 27, 30, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533667516 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 Building ZINC001533667516 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533667516 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 850) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 18, 35, 35, 35, 35, 35, 35, 35, 35, 41, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 851) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 3, 3, 15, 27, 27, 30, 30, 27, 30, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 852) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 18, 35, 35, 35, 35, 35, 35, 35, 35, 41, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 853) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1) `ZINC001533667516.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533667516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001533667516 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccc(Cl)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 3, 3, 15, 27, 27, 30, 30, 27, 30, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533667516 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533667516 Building ZINC001533690452 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533690452 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/854 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/855 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 13, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/856 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/856' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 9, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/857 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/857' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 8, 12, 12, 12, 12, 12, 31, 32, 32, 32, 32, 32, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 12, 12, 12, 12, 31, 31, 32, 32, 32, 32, 32, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533690452 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 Building ZINC001533690452 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533690452 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 854) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 855) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 13, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 856) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 9, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 857) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 8, 12, 12, 12, 12, 12, 31, 32, 32, 32, 32, 32, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 12, 12, 12, 12, 31, 31, 32, 32, 32, 32, 32, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533690452 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 Building ZINC001533690452 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533690452 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 854) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 855) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 13, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 856) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 9, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 857) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 8, 12, 12, 12, 12, 12, 31, 32, 32, 32, 32, 32, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 12, 12, 12, 12, 31, 31, 32, 32, 32, 32, 32, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533690452 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 Building ZINC001533690452 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533690452 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 854) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 855) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 13, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 856) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 9, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 857) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690452.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533690452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690452 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 8, 12, 12, 12, 12, 12, 31, 32, 32, 32, 32, 32, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 12, 12, 12, 12, 31, 31, 32, 32, 32, 32, 32, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533690452 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690452 Building ZINC001533690455 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533690455 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/858 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 8, 15, 15, 15, 15, 15, 33, 35, 35, 33, 35, 35, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 15, 15, 15, 15, 33, 33, 35, 35, 33, 35, 35, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/859 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 8, 15, 15, 15, 15, 15, 34, 36, 36, 35, 36, 36, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 15, 15, 15, 15, 34, 34, 36, 36, 35, 36, 36, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/860 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/860' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/861 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/861' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533690455 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 Building ZINC001533690455 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533690455 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 858) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 8, 15, 15, 15, 15, 15, 33, 35, 35, 33, 35, 35, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 15, 15, 15, 15, 33, 33, 35, 35, 33, 35, 35, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 859) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 8, 15, 15, 15, 15, 15, 34, 36, 36, 35, 36, 36, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 15, 15, 15, 15, 34, 34, 36, 36, 35, 36, 36, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 860) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 861) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533690455 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 Building ZINC001533690455 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533690455 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 858) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 8, 15, 15, 15, 15, 15, 33, 35, 35, 33, 35, 35, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 15, 15, 15, 15, 33, 33, 35, 35, 33, 35, 35, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 859) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 8, 15, 15, 15, 15, 15, 34, 36, 36, 35, 36, 36, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 15, 15, 15, 15, 34, 34, 36, 36, 35, 36, 36, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 860) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 861) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533690455 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 Building ZINC001533690455 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533690455 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 858) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 8, 15, 15, 15, 15, 15, 33, 35, 35, 33, 35, 35, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 15, 15, 15, 15, 33, 33, 35, 35, 33, 35, 35, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 859) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 8, 15, 15, 15, 15, 15, 34, 36, 36, 35, 36, 36, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 15, 15, 15, 15, 34, 34, 36, 36, 35, 36, 36, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 860) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 861) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001533690455.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533690455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533690455 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533690455 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533690455 Building ZINC001533696671 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533696671 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/862 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C(F)(F)F)c1)c1ccccc1) `ZINC001533696671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533696671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001533696671 none O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C(F)(F)F)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 11, 6, 16, 16, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 43, 50, 50, 50, 50, 50, 43, 16, 16, 6, 3, 3, 3, 3, 16, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/863 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C(F)(F)F)c1)c1ccccc1) `ZINC001533696671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533696671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001533696671 none O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C(F)(F)F)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 12, 8, 16, 16, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 46, 50, 50, 46, 50, 50, 46, 16, 16, 6, 3, 3, 3, 3, 16, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533696671 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 Building ZINC001533696671 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533696671 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 862) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C(F)(F)F)c1)c1ccccc1) `ZINC001533696671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533696671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001533696671 none O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C(F)(F)F)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 11, 6, 16, 16, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 43, 50, 50, 50, 50, 50, 43, 16, 16, 6, 3, 3, 3, 3, 16, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 863) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C(F)(F)F)c1)c1ccccc1) `ZINC001533696671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533696671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001533696671 none O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C(F)(F)F)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 12, 8, 16, 16, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 46, 50, 50, 46, 50, 50, 46, 16, 16, 6, 3, 3, 3, 3, 16, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533696671 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533696671 Building ZINC001533714706 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533714706 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/864 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(C)cc(C)c1) `ZINC001533714706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533714706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001533714706 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(C)cc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 15, 12, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/865 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(C)cc(C)c1) `ZINC001533714706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533714706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001533714706 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(C)cc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 9, 15, 15, 15, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 9, 9, 15, 15, 15, 15, 9, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533714706 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 Building ZINC001533714706 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533714706 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 864) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(C)cc(C)c1) `ZINC001533714706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533714706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001533714706 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(C)cc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 15, 12, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 865) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(C)cc(C)c1) `ZINC001533714706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533714706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001533714706 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(C)cc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 9, 15, 15, 15, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 9, 9, 15, 15, 15, 15, 9, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533714706 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533714706 Building ZINC001533723348 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533723348 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/866 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1) `ZINC001533723348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533723348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001533723348 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 14, 28, 28, 16, 28, 28, 28, 14, 14, 14, 14, 14, 14, 6, 10, 10, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/867 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1) `ZINC001533723348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533723348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001533723348 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 14, 28, 28, 17, 28, 28, 28, 14, 14, 14, 14, 14, 14, 6, 10, 10, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533723348 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 Building ZINC001533723348 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533723348 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 866) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1) `ZINC001533723348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533723348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001533723348 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 14, 28, 28, 16, 28, 28, 28, 14, 14, 14, 14, 14, 14, 6, 10, 10, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 867) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1) `ZINC001533723348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533723348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001533723348 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 14, 28, 28, 17, 28, 28, 28, 14, 14, 14, 14, 14, 14, 6, 10, 10, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533723348 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533723348 Building ZINC001533742803 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533742803 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/868 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCC1CC1)CC1CC1) `ZINC001533742803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533742803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001533742803 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCC1CC1)CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 6, 10, 10, 3, 4, 7, 7, 1, 1, 1, 9, 9, 1, 9, 1, 1, 1, 5, 5, 7, 7, 10, 10, 10, 10, 10, 4, 4, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 40, 14, 15, 16, 17, 18, 19, 39, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/869 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCC1CC1)CC1CC1) `ZINC001533742803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533742803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001533742803 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCC1CC1)CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 7, 13, 13, 2, 6, 7, 7, 1, 1, 1, 10, 10, 1, 10, 1, 1, 1, 6, 6, 8, 8, 13, 13, 13, 13, 13, 6, 6, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 40, 14, 15, 16, 17, 18, 19, 20, 21, 39, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533742803 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 Building ZINC001533742803 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533742803 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 868) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCC1CC1)CC1CC1) `ZINC001533742803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533742803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001533742803 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCC1CC1)CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 6, 10, 10, 3, 4, 7, 7, 1, 1, 1, 9, 9, 1, 9, 1, 1, 1, 5, 5, 7, 7, 10, 10, 10, 10, 10, 4, 4, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 40, 14, 15, 16, 17, 18, 19, 39, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 869) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCC1CC1)CC1CC1) `ZINC001533742803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533742803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001533742803 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCC1CC1)CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 7, 13, 13, 2, 6, 7, 7, 1, 1, 1, 10, 10, 1, 10, 1, 1, 1, 6, 6, 8, 8, 13, 13, 13, 13, 13, 6, 6, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 40, 14, 15, 16, 17, 18, 19, 20, 21, 39, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533742803 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533742803 Building ZINC001533773583 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533773583 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/870 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2c(Cl)cccc2Cl)cc1Cl) `ZINC001533773583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533773583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533773583 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2c(Cl)cccc2Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 8, 8, 8, 4, 4, 3, 8, 8, 21, 21, 21, 21, 21, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/871 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2c(Cl)cccc2Cl)cc1Cl) `ZINC001533773583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533773583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533773583 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2c(Cl)cccc2Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 9, 9, 9, 5, 5, 3, 8, 8, 21, 21, 21, 21, 21, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533773583 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 Building ZINC001533773583 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533773583 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 870) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2c(Cl)cccc2Cl)cc1Cl) `ZINC001533773583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533773583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533773583 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2c(Cl)cccc2Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 8, 8, 8, 4, 4, 3, 8, 8, 21, 21, 21, 21, 21, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 871) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2c(Cl)cccc2Cl)cc1Cl) `ZINC001533773583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533773583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533773583 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2c(Cl)cccc2Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 9, 9, 9, 5, 5, 3, 8, 8, 21, 21, 21, 21, 21, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533773583 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533773583 Building ZINC001533779109 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533779109 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/872 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)C(=O)OC(C)(C)C) `ZINC001533779109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533779109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533779109 none CCN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 12, 4, 4, 4, 3, 8, 8, 12, 19, 19, 19, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 4, 4, 12, 12, 12, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/873 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)C(=O)OC(C)(C)C) `ZINC001533779109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533779109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533779109 none CCN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 3, 4, 4, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 9, 4, 4, 4, 4, 12, 12, 19, 23, 23, 23, 7, 7, 7, 7, 7, 4, 4, 4, 3, 4, 4, 3, 4, 4, 9, 9, 9, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533779109 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 Building ZINC001533779109 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533779109 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 872) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)C(=O)OC(C)(C)C) `ZINC001533779109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533779109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533779109 none CCN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 12, 4, 4, 4, 3, 8, 8, 12, 19, 19, 19, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 4, 4, 12, 12, 12, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 873) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)C(=O)OC(C)(C)C) `ZINC001533779109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533779109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001533779109 none CCN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 3, 4, 4, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 9, 4, 4, 4, 4, 12, 12, 19, 23, 23, 23, 7, 7, 7, 7, 7, 4, 4, 4, 3, 4, 4, 3, 4, 4, 9, 9, 9, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533779109 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533779109 Building ZINC001533786191 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533786191 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/874 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(Br)c2)cc1Cl) `ZINC001533786191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533786191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001533786191 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 2, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 13, 13, 13, 10, 10, 10, 19, 19, 19, 10, 10, 4, 13, 4, 13, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/875 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(Br)c2)cc1Cl) `ZINC001533786191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533786191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001533786191 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 2, 10, 10, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 12, 12, 12, 10, 10, 10, 19, 19, 19, 10, 10, 4, 12, 4, 12, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533786191 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 Building ZINC001533786191 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533786191 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 874) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(Br)c2)cc1Cl) `ZINC001533786191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533786191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001533786191 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 2, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 13, 13, 13, 10, 10, 10, 19, 19, 19, 10, 10, 4, 13, 4, 13, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 875) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(Br)c2)cc1Cl) `ZINC001533786191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533786191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001533786191 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 2, 10, 10, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 12, 12, 12, 10, 10, 10, 19, 19, 19, 10, 10, 4, 12, 4, 12, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533786191 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533786191 Building ZINC001533812289 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533812289 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/876 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 4, 12, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 31, 31, 27, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/877 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 4, 12, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 31, 31, 27, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/878 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/878' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 26, 29, 29, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/879 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/879' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 26, 29, 29, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533812289 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 Building ZINC001533812289 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533812289 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 876) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 4, 12, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 31, 31, 27, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 877) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 4, 12, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 31, 31, 27, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 878) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 26, 29, 29, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 879) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 26, 29, 29, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533812289 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 Building ZINC001533812289 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533812289 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 876) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 4, 12, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 31, 31, 27, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 877) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 4, 12, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 31, 31, 27, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 878) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 26, 29, 29, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 879) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 26, 29, 29, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533812289 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 Building ZINC001533812289 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001533812289 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 876) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 4, 12, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 31, 31, 27, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 877) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 4, 12, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 27, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 31, 31, 27, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `2' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 2 (index: 878) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 26, 29, 29, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `3' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 3 (index: 879) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1) `ZINC001533812289.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001533812289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001533812289 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)CN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 10, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 26, 29, 29, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533812289 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/1.* 3: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/3.* 2: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289/2.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533812289 Building ZINC001533818993 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533818993 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/880 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533818993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533818993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533818993 none COC(=O)[C@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 20, 33, 6, 20, 20, 29, 29, 29, 29, 29, 29, 29, 4, 6, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 33, 33, 33, 29, 29, 29, 6, 6, 6, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/881 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533818993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533818993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533818993 none COC(=O)[C@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 22, 37, 5, 22, 22, 30, 30, 30, 30, 30, 30, 30, 3, 5, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 37, 37, 37, 30, 30, 30, 5, 5, 5, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533818993 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 Building ZINC001533818993 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533818993 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 880) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1cccc(Cl)c1Cl)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533818993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533818993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533818993 none COC(=O)[C@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 20, 33, 6, 20, 20, 29, 29, 29, 29, 29, 29, 29, 4, 6, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 33, 33, 33, 29, 29, 29, 6, 6, 6, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 881) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1cccc(Cl)c1Cl)N(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533818993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533818993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533818993 none COC(=O)[C@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 22, 37, 5, 22, 22, 30, 30, 30, 30, 30, 30, 30, 3, 5, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 37, 37, 37, 30, 30, 30, 5, 5, 5, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533818993 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818993 Building ZINC001533818997 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533818997 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/882 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533818997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533818997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533818997 none COC(=O)[C@@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 22, 37, 5, 22, 22, 30, 30, 26, 30, 30, 30, 30, 3, 5, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 37, 37, 37, 30, 30, 30, 5, 5, 5, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/883 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533818997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533818997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533818997 none COC(=O)[C@@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 19, 32, 6, 19, 19, 29, 29, 29, 29, 29, 29, 29, 4, 6, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 29, 29, 29, 6, 6, 6, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533818997 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 Building ZINC001533818997 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533818997 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 882) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1cccc(Cl)c1Cl)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533818997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533818997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533818997 none COC(=O)[C@@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 22, 37, 5, 22, 22, 30, 30, 26, 30, 30, 30, 30, 3, 5, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 37, 37, 37, 30, 30, 30, 5, 5, 5, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 883) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1cccc(Cl)c1Cl)N(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001533818997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533818997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001533818997 none COC(=O)[C@@H](c1cccc(Cl)c1Cl)N(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 19, 32, 6, 19, 19, 29, 29, 29, 29, 29, 29, 29, 4, 6, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 29, 29, 29, 6, 6, 6, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533818997 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533818997 Building ZINC001533827729 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533827729 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/884 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(c2ccc(Br)cc2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001533827729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533827729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533827729 none O=C(Nc1csc(c2ccc(Br)cc2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 15, 15, 15, 15, 19, 19, 15, 17, 19, 19, 15, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 8, 15, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/885 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(c2ccc(Br)cc2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001533827729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533827729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533827729 none O=C(Nc1csc(c2ccc(Br)cc2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 16, 16, 16, 16, 19, 19, 16, 16, 19, 19, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 8, 16, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533827729 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 Building ZINC001533827729 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533827729 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 884) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(c2ccc(Br)cc2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001533827729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533827729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533827729 none O=C(Nc1csc(c2ccc(Br)cc2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 15, 15, 15, 15, 19, 19, 15, 17, 19, 19, 15, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 8, 15, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 885) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(c2ccc(Br)cc2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001533827729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533827729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001533827729 none O=C(Nc1csc(c2ccc(Br)cc2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 16, 16, 16, 16, 19, 19, 16, 16, 19, 19, 16, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 8, 16, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533827729 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533827729 Building ZINC001533831048 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533831048 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/886 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)c2ccccc2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533831048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533831048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533831048 none Cc1ccc(NC(=O)c2ccccc2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 20, 20, 20, 27, 27, 26, 27, 27, 9, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 27, 27, 27, 27, 27, 9, 4, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/887 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)c2ccccc2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533831048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533831048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533831048 none Cc1ccc(NC(=O)c2ccccc2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 22, 22, 22, 30, 30, 25, 30, 30, 10, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 22, 30, 30, 30, 30, 30, 10, 4, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533831048 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 Building ZINC001533831048 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533831048 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 886) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)c2ccccc2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533831048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533831048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533831048 none Cc1ccc(NC(=O)c2ccccc2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 20, 20, 20, 27, 27, 26, 27, 27, 9, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 27, 27, 27, 27, 27, 9, 4, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 887) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)c2ccccc2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533831048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533831048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533831048 none Cc1ccc(NC(=O)c2ccccc2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 22, 22, 22, 30, 30, 25, 30, 30, 10, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 22, 30, 30, 30, 30, 30, 10, 4, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533831048 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533831048 Building ZINC001533853757 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533853757 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/888 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccccc1Oc1cccc(Cl)c1) `ZINC001533853757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533853757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533853757 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccccc1Oc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 6, 6, 10, 10, 6, 10, 10, 10, 21, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 10, 10, 10, 10, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/889 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccccc1Oc1cccc(Cl)c1) `ZINC001533853757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533853757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533853757 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccccc1Oc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 17, 17, 13, 17, 17, 17, 29, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 13, 13, 13, 17, 17, 17, 17, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 137 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533853757 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 Building ZINC001533853757 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533853757 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 888) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccccc1Oc1cccc(Cl)c1) `ZINC001533853757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533853757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533853757 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccccc1Oc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 6, 6, 10, 10, 6, 10, 10, 10, 21, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 10, 10, 10, 10, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 889) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccccc1Oc1cccc(Cl)c1) `ZINC001533853757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533853757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533853757 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccccc1Oc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 17, 17, 13, 17, 17, 17, 29, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 13, 13, 13, 17, 17, 17, 17, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 137 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533853757 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853757 Building ZINC001533853760 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533853760 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/890 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccccc1Oc1cccc(Cl)c1) `ZINC001533853760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533853760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533853760 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccccc1Oc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 18, 18, 13, 18, 18, 18, 28, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 13, 13, 13, 18, 18, 18, 18, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/891 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccccc1Oc1cccc(Cl)c1) `ZINC001533853760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533853760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533853760 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccccc1Oc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 4, 7, 7, 7, 10, 10, 7, 10, 10, 10, 21, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 7, 10, 10, 10, 10, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533853760 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 Building ZINC001533853760 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533853760 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 890) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccccc1Oc1cccc(Cl)c1) `ZINC001533853760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533853760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533853760 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccccc1Oc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 18, 18, 13, 18, 18, 18, 28, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 13, 13, 13, 18, 18, 18, 18, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 891) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccccc1Oc1cccc(Cl)c1) `ZINC001533853760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533853760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001533853760 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccccc1Oc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 4, 7, 7, 7, 10, 10, 7, 10, 10, 10, 21, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 7, 10, 10, 10, 10, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533853760 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533853760 Building ZINC001533861232 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533861232 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/892 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Oc3ccc(F)c(C)c3)cc2Cl)cn1) `ZINC001533861232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533861232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001533861232 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Oc3ccc(F)c(C)c3)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 14, 35, 35, 34, 35, 35, 35, 35, 3, 3, 3, 2, 2, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 3, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/893 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Oc3ccc(F)c(C)c3)cc2Cl)cn1) `ZINC001533861232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533861232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001533861232 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Oc3ccc(F)c(C)c3)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 5, 5, 5, 5, 5, 17, 35, 35, 17, 17, 35, 35, 35, 5, 5, 5, 2, 2, 4, 4, 4, 4, 4, 2, 3, 3, 3, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533861232 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 Building ZINC001533861232 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533861232 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 892) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Oc3ccc(F)c(C)c3)cc2Cl)cn1) `ZINC001533861232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533861232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001533861232 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Oc3ccc(F)c(C)c3)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 14, 35, 35, 34, 35, 35, 35, 35, 3, 3, 3, 2, 2, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 3, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 893) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Oc3ccc(F)c(C)c3)cc2Cl)cn1) `ZINC001533861232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533861232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001533861232 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Oc3ccc(F)c(C)c3)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 5, 5, 5, 5, 5, 17, 35, 35, 17, 17, 35, 35, 35, 5, 5, 5, 2, 2, 4, 4, 4, 4, 4, 2, 3, 3, 3, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533861232 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533861232 Building ZINC001533904352 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533904352 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/894 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)n(c3ccc(C)cc3)n2)c1) `ZINC001533904352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533904352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001533904352 none COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 8, 8, 8, 4, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 47, 50, 50, 50, 47, 47, 47, 8, 4, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 47] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/895 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)n(c3ccc(C)cc3)n2)c1) `ZINC001533904352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533904352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001533904352 none COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 8, 8, 8, 4, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 47, 50, 50, 50, 47, 47, 47, 8, 4, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 47] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533904352 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 Building ZINC001533904352 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533904352 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 894) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)n(c3ccc(C)cc3)n2)c1) `ZINC001533904352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533904352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001533904352 none COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 8, 8, 8, 4, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 47, 50, 50, 50, 47, 47, 47, 8, 4, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 47] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 895) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)n(c3ccc(C)cc3)n2)c1) `ZINC001533904352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533904352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001533904352 none COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 8, 8, 8, 4, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 47, 50, 50, 50, 47, 47, 47, 8, 4, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 47] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533904352 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533904352 Building ZINC001533905363 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533905363 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/896 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)n(c3ccccc3)n2)c1) `ZINC001533905363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533905363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001533905363 none COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)n(c3ccccc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 6, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/897 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)n(c3ccccc3)n2)c1) `ZINC001533905363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533905363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001533905363 none COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)n(c3ccccc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 6, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533905363 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 Building ZINC001533905363 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533905363 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 896) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)n(c3ccccc3)n2)c1) `ZINC001533905363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533905363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001533905363 none COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)n(c3ccccc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 6, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 897) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)n(c3ccccc3)n2)c1) `ZINC001533905363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533905363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001533905363 none COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)n(c3ccccc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 6, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533905363 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533905363 Building ZINC001533919362 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533919362 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/898 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1noc(c2cc(Cl)ccc2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC001533919362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533919362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001533919362 none CC(C)Cc1noc(c2cc(Cl)ccc2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/899 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1noc(c2cc(Cl)ccc2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC001533919362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533919362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001533919362 none CC(C)Cc1noc(c2cc(Cl)ccc2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533919362 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 Building ZINC001533919362 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533919362 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 898) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1noc(c2cc(Cl)ccc2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC001533919362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533919362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001533919362 none CC(C)Cc1noc(c2cc(Cl)ccc2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 899) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1noc(c2cc(Cl)ccc2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC001533919362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533919362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001533919362 none CC(C)Cc1noc(c2cc(Cl)ccc2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533919362 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533919362 Building ZINC001533920824 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533920824 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/900 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533920824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533920824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533920824 none O=C(NCc1ccc(OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 25, 25, 17, 25, 38, 38, 49, 49, 38, 49, 49, 25, 25, 1, 1, 1, 4, 4, 4, 4, 4, 2, 13, 13, 25, 25, 38, 38, 49, 49, 38, 49, 49, 25, 25, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/901 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533920824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533920824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533920824 none O=C(NCc1ccc(OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 25, 25, 13, 13, 38, 38, 49, 49, 38, 49, 49, 25, 25, 1, 1, 1, 4, 4, 4, 4, 4, 2, 13, 13, 25, 25, 38, 38, 49, 49, 38, 49, 49, 25, 25, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533920824 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 Building ZINC001533920824 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533920824 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 900) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533920824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533920824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533920824 none O=C(NCc1ccc(OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 25, 25, 17, 25, 38, 38, 49, 49, 38, 49, 49, 25, 25, 1, 1, 1, 4, 4, 4, 4, 4, 2, 13, 13, 25, 25, 38, 38, 49, 49, 38, 49, 49, 25, 25, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 901) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533920824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533920824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001533920824 none O=C(NCc1ccc(OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 25, 25, 13, 13, 38, 38, 49, 49, 38, 49, 49, 25, 25, 1, 1, 1, 4, 4, 4, 4, 4, 2, 13, 13, 25, 25, 38, 38, 49, 49, 38, 49, 49, 25, 25, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533920824 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533920824 Building ZINC001533929412 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533929412 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/902 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(C(F)(F)F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC001533929412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533929412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533929412 none Cc1cc(C)n(c2ccc(C(F)(F)F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/903 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(C(F)(F)F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC001533929412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533929412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533929412 none Cc1cc(C)n(c2ccc(C(F)(F)F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 11, 11, 11, 8, 11, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533929412 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 Building ZINC001533929412 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533929412 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 902) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(C(F)(F)F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC001533929412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533929412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533929412 none Cc1cc(C)n(c2ccc(C(F)(F)F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 903) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(C(F)(F)F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC001533929412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533929412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533929412 none Cc1cc(C)n(c2ccc(C(F)(F)F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 11, 11, 11, 8, 11, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533929412 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533929412 Building ZINC001533934709 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533934709 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/904 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC/C=C/c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533934709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533934709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001533934709 none O=C(NCC/C=C/c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 23, 45, 45, 47, 47, 45, 45, 47, 47, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 23, 23, 45, 45, 47, 47, 47, 47, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/905 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC/C=C/c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533934709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533934709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001533934709 none O=C(NCC/C=C/c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 22, 44, 44, 46, 46, 44, 44, 46, 46, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 22, 22, 44, 44, 46, 46, 46, 46, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533934709 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 Building ZINC001533934709 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533934709 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 904) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC/C=C/c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533934709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533934709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001533934709 none O=C(NCC/C=C/c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 23, 45, 45, 47, 47, 45, 45, 47, 47, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 23, 23, 45, 45, 47, 47, 47, 47, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 905) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC/C=C/c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533934709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533934709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001533934709 none O=C(NCC/C=C/c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 22, 44, 44, 46, 46, 44, 44, 46, 46, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 22, 22, 44, 44, 46, 46, 46, 46, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533934709 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533934709 Building ZINC001533937611 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533937611 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/906 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncc(Cc3ccc(Br)c(C)c3)s2)cc1) `ZINC001533937611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533937611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001533937611 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncc(Cc3ccc(Br)c(C)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 17, 1, 5, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 4, 3, 3, 3, 3, 3, 3, 3, 2, 4, 26, 26, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/907 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncc(Cc3ccc(Br)c(C)c3)s2)cc1) `ZINC001533937611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533937611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001533937611 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncc(Cc3ccc(Br)c(C)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 17, 1, 5, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 4, 3, 3, 3, 3, 3, 3, 3, 2, 4, 26, 26, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533937611 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 Building ZINC001533937611 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533937611 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 906) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncc(Cc3ccc(Br)c(C)c3)s2)cc1) `ZINC001533937611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533937611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001533937611 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncc(Cc3ccc(Br)c(C)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 17, 1, 5, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 4, 3, 3, 3, 3, 3, 3, 3, 2, 4, 26, 26, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 907) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncc(Cc3ccc(Br)c(C)c3)s2)cc1) `ZINC001533937611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533937611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001533937611 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncc(Cc3ccc(Br)c(C)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 17, 1, 5, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 4, 3, 3, 3, 3, 3, 3, 3, 2, 4, 26, 26, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533937611 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533937611 Building ZINC001533946184 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533946184 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/908 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533946184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533946184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533946184 none O=C(NCCc1cccc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 16, 25, 25, 25, 25, 25, 28, 28, 46, 46, 33, 46, 46, 25, 1, 1, 1, 5, 5, 5, 5, 5, 3, 11, 11, 16, 16, 25, 25, 25, 28, 28, 46, 46, 46, 46, 46, 25, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 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/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/909 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533946184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533946184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533946184 none O=C(NCCc1cccc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 16, 25, 25, 25, 25, 25, 28, 28, 46, 46, 30, 46, 46, 25, 1, 1, 1, 5, 5, 5, 5, 5, 3, 11, 11, 16, 16, 25, 25, 25, 28, 28, 46, 46, 46, 46, 46, 25, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533946184 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 Building ZINC001533946184 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533946184 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 908) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533946184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533946184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533946184 none O=C(NCCc1cccc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 16, 25, 25, 25, 25, 25, 28, 28, 46, 46, 33, 46, 46, 25, 1, 1, 1, 5, 5, 5, 5, 5, 3, 11, 11, 16, 16, 25, 25, 25, 28, 28, 46, 46, 46, 46, 46, 25, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 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/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 909) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533946184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533946184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001533946184 none O=C(NCCc1cccc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 16, 25, 25, 25, 25, 25, 28, 28, 46, 46, 30, 46, 46, 25, 1, 1, 1, 5, 5, 5, 5, 5, 3, 11, 11, 16, 16, 25, 25, 25, 28, 28, 46, 46, 46, 46, 46, 25, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533946184 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533946184 Building ZINC001533956401 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533956401 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/910 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2noc(C3CCCCC3)n2)CCCCCC1) `ZINC001533956401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533956401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533956401 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2noc(C3CCCCC3)n2)CCCCCC1 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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 12, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 4, 8, 24, 24, 24, 25, 50, 50, 50, 50, 50, 24, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 10, 7, 34, 35, 36, 5, 37, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/911 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2noc(C3CCCCC3)n2)CCCCCC1) `ZINC001533956401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533956401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533956401 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2noc(C3CCCCC3)n2)CCCCCC1 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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 12, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 6, 10, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533956401 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 Building ZINC001533956401 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533956401 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 910) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2noc(C3CCCCC3)n2)CCCCCC1) `ZINC001533956401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533956401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533956401 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2noc(C3CCCCC3)n2)CCCCCC1 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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 12, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 4, 8, 24, 24, 24, 25, 50, 50, 50, 50, 50, 24, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 10, 7, 34, 35, 36, 5, 37, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 911) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2noc(C3CCCCC3)n2)CCCCCC1) `ZINC001533956401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533956401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001533956401 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2noc(C3CCCCC3)n2)CCCCCC1 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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 12, 1, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 6, 10, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533956401 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533956401 Building ZINC001533978512 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533978512 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/912 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2ccccc2F)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533978512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533978512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001533978512 none O=C(Nc1ncc(Cc2ccccc2F)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 24, 39, 39, 24, 39, 39, 39, 4, 1, 1, 1, 6, 6, 6, 6, 6, 2, 4, 24, 24, 39, 39, 36, 39, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/913 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2ccccc2F)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533978512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533978512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001533978512 none O=C(Nc1ncc(Cc2ccccc2F)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 25, 39, 39, 35, 39, 39, 39, 5, 1, 1, 1, 6, 6, 6, 6, 6, 3, 5, 25, 25, 39, 39, 39, 39, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533978512 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 Building ZINC001533978512 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533978512 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 912) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2ccccc2F)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533978512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533978512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001533978512 none O=C(Nc1ncc(Cc2ccccc2F)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 24, 39, 39, 24, 39, 39, 39, 4, 1, 1, 1, 6, 6, 6, 6, 6, 2, 4, 24, 24, 39, 39, 36, 39, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 913) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2ccccc2F)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001533978512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533978512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001533978512 none O=C(Nc1ncc(Cc2ccccc2F)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 25, 39, 39, 35, 39, 39, 39, 5, 1, 1, 1, 6, 6, 6, 6, 6, 3, 5, 25, 25, 39, 39, 39, 39, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533978512 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533978512 Building ZINC001533994274 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533994274 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/914 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](COc2ccccc2F)c2ccccc2)cc1Cl) `ZINC001533994274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533994274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001533994274 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](COc2ccccc2F)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 12, 24, 30, 30, 24, 30, 30, 30, 4, 5, 5, 5, 5, 5, 4, 4, 4, 10, 10, 10, 4, 4, 2, 12, 12, 30, 30, 25, 30, 5, 5, 5, 5, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/915 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](COc2ccccc2F)c2ccccc2)cc1Cl) `ZINC001533994274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533994274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001533994274 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](COc2ccccc2F)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 22, 29, 29, 24, 29, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 8, 8, 29, 29, 28, 29, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533994274 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 Building ZINC001533994274 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533994274 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 914) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](COc2ccccc2F)c2ccccc2)cc1Cl) `ZINC001533994274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533994274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001533994274 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](COc2ccccc2F)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 12, 24, 30, 30, 24, 30, 30, 30, 4, 5, 5, 5, 5, 5, 4, 4, 4, 10, 10, 10, 4, 4, 2, 12, 12, 30, 30, 25, 30, 5, 5, 5, 5, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 915) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](COc2ccccc2F)c2ccccc2)cc1Cl) `ZINC001533994274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533994274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001533994274 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](COc2ccccc2F)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 22, 29, 29, 24, 29, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 8, 8, 29, 29, 28, 29, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533994274 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994274 Building ZINC001533994275 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533994275 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/916 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](COc2ccccc2F)c2ccccc2)cc1Cl) `ZINC001533994275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533994275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001533994275 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](COc2ccccc2F)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 22, 28, 28, 23, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 8, 8, 28, 28, 27, 28, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/917 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](COc2ccccc2F)c2ccccc2)cc1Cl) `ZINC001533994275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533994275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001533994275 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](COc2ccccc2F)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 12, 23, 29, 29, 23, 29, 29, 29, 4, 5, 5, 4, 5, 5, 4, 4, 4, 10, 10, 10, 4, 4, 2, 12, 12, 29, 29, 24, 29, 5, 5, 4, 5, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 134 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533994275 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 Building ZINC001533994275 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533994275 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 916) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](COc2ccccc2F)c2ccccc2)cc1Cl) `ZINC001533994275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533994275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001533994275 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](COc2ccccc2F)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 22, 28, 28, 23, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 8, 8, 28, 28, 27, 28, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 917) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](COc2ccccc2F)c2ccccc2)cc1Cl) `ZINC001533994275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533994275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001533994275 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](COc2ccccc2F)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 12, 23, 29, 29, 23, 29, 29, 29, 4, 5, 5, 4, 5, 5, 4, 4, 4, 10, 10, 10, 4, 4, 2, 12, 12, 29, 29, 24, 29, 5, 5, 4, 5, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 134 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533994275 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533994275 Building ZINC001533998067 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533998067 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/918 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCSCC(C)C) `ZINC001533998067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533998067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533998067 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCSCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 8, 10, 16, 20, 20, 20, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/919 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCSCC(C)C) `ZINC001533998067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533998067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533998067 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCSCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 11, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533998067 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 Building ZINC001533998067 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001533998067 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 918) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCSCC(C)C) `ZINC001533998067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001533998067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533998067 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCSCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 8, 10, 16, 20, 20, 20, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 919) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCSCC(C)C) `ZINC001533998067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001533998067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001533998067 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCSCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 11, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001533998067 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001533998067 Building ZINC001534058382 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534058382 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/920 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccnc1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534058382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534058382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534058382 none O=C(N(Cc1cccnc1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 14, 35, 35, 35, 35, 35, 6, 10, 10, 9, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 35, 35, 35, 35, 10, 10, 10, 10, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/921 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccnc1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534058382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534058382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534058382 none O=C(N(Cc1cccnc1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 15, 35, 35, 35, 35, 35, 6, 11, 11, 8, 9, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 35, 35, 35, 35, 11, 11, 11, 11, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534058382 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 Building ZINC001534058382 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534058382 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 920) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccnc1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534058382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534058382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534058382 none O=C(N(Cc1cccnc1)c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 14, 35, 35, 35, 35, 35, 6, 10, 10, 9, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 35, 35, 35, 35, 10, 10, 10, 10, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 921) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccnc1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534058382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534058382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534058382 none O=C(N(Cc1cccnc1)c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 15, 35, 35, 35, 35, 35, 6, 11, 11, 8, 9, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 35, 35, 35, 35, 11, 11, 11, 11, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534058382 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534058382 Building ZINC001534070690 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534070690 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/922 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001534070690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534070690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534070690 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 44, 50, 50, 50, 50, 50, 50, 50, 44, 44, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 50, 50, 50, 44, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/923 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001534070690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534070690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534070690 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 44, 50, 50, 44, 50, 50, 50, 50, 44, 44, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 17, 17, 50, 50, 50, 44, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534070690 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 Building ZINC001534070690 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534070690 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 922) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001534070690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534070690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534070690 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 44, 50, 50, 50, 50, 50, 50, 50, 44, 44, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 50, 50, 50, 44, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 923) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001534070690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534070690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534070690 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 17, 44, 50, 50, 44, 50, 50, 50, 50, 44, 44, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 17, 17, 50, 50, 50, 44, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534070690 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534070690 Building ZINC001534080037 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534080037 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/924 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534080037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534080037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001534080037 none O=C(NCCc1ccc(OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 17, 17, 17, 17, 17, 28, 28, 38, 38, 28, 38, 38, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 3, 12, 12, 17, 17, 17, 17, 28, 28, 38, 38, 28, 38, 38, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/925 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534080037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534080037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001534080037 none O=C(NCCc1ccc(OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 16, 16, 16, 16, 16, 26, 26, 38, 38, 26, 38, 38, 16, 16, 1, 1, 1, 7, 7, 7, 7, 7, 3, 12, 12, 16, 16, 16, 16, 26, 26, 38, 38, 26, 38, 38, 16, 16, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534080037 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 Building ZINC001534080037 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534080037 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 924) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534080037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534080037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001534080037 none O=C(NCCc1ccc(OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 17, 17, 17, 17, 17, 28, 28, 38, 38, 28, 38, 38, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 3, 12, 12, 17, 17, 17, 17, 28, 28, 38, 38, 28, 38, 38, 17, 17, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 925) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534080037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534080037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001534080037 none O=C(NCCc1ccc(OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 16, 16, 16, 16, 16, 26, 26, 38, 38, 26, 38, 38, 16, 16, 1, 1, 1, 7, 7, 7, 7, 7, 3, 12, 12, 16, 16, 16, 16, 26, 26, 38, 38, 26, 38, 38, 16, 16, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534080037 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534080037 Building ZINC001534082295 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534082295 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/926 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)c3ccc(F)cc3)cccc21) `ZINC001534082295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534082295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534082295 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)c3ccc(F)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 10, 16, 19, 19, 19, 19, 19, 19, 45, 45, 45, 46, 46, 45, 46, 46, 46, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 45, 46, 46, 46, 46, 19, 19, 19] 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]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/927 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)c3ccc(F)cc3)cccc21) `ZINC001534082295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534082295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534082295 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)c3ccc(F)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 10, 16, 18, 18, 18, 18, 18, 18, 47, 47, 47, 50, 50, 47, 49, 50, 50, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 47, 50, 50, 50, 50, 18, 18, 18] 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]) total number of confs: 141 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534082295 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 Building ZINC001534082295 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534082295 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 926) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)c3ccc(F)cc3)cccc21) `ZINC001534082295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534082295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534082295 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)c3ccc(F)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 10, 16, 19, 19, 19, 19, 19, 19, 45, 45, 45, 46, 46, 45, 46, 46, 46, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 45, 46, 46, 46, 46, 19, 19, 19] 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]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 927) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)c3ccc(F)cc3)cccc21) `ZINC001534082295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534082295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534082295 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)c3ccc(F)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 10, 16, 18, 18, 18, 18, 18, 18, 47, 47, 47, 50, 50, 47, 49, 50, 50, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 47, 50, 50, 50, 50, 18, 18, 18] 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]) total number of confs: 141 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534082295 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534082295 Building ZINC001534089321 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534089321 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/928 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1cccs1) `ZINC001534089321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534089321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534089321 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 6, 6, 6, 7, 12, 12, 12, 12, 3, 3, 3, 13, 13, 7, 13, 3, 3, 3, 4, 4, 4, 6, 6, 6, 7, 7, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/929 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1cccs1) `ZINC001534089321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534089321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534089321 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534089321 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 Building ZINC001534089321 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534089321 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 928) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1cccs1) `ZINC001534089321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534089321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534089321 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 6, 6, 6, 7, 12, 12, 12, 12, 3, 3, 3, 13, 13, 7, 13, 3, 3, 3, 4, 4, 4, 6, 6, 6, 7, 7, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 929) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1cccs1) `ZINC001534089321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534089321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534089321 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534089321 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089321 Building ZINC001534089322 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534089322 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/930 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1cccs1) `ZINC001534089322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534089322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534089322 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 63 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/931 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1cccs1) `ZINC001534089322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534089322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534089322 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 9, 13, 13, 13, 13, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 8, 8, 8, 9, 9, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534089322 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 Building ZINC001534089322 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534089322 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 930) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1cccs1) `ZINC001534089322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534089322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534089322 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 63 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 931) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1cccs1) `ZINC001534089322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534089322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534089322 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1cccs1 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 9, 13, 13, 13, 13, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 8, 8, 8, 9, 9, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534089322 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534089322 Building ZINC001534145796 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534145796 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/932 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Sc2nsc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)cc1) `ZINC001534145796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534145796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534145796 none COc1ccc(Sc2nsc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/933 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Sc2nsc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)cc1) `ZINC001534145796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534145796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534145796 none COc1ccc(Sc2nsc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 31, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534145796 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 Building ZINC001534145796 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534145796 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 932) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Sc2nsc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)cc1) `ZINC001534145796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534145796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534145796 none COc1ccc(Sc2nsc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 933) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Sc2nsc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)cc1) `ZINC001534145796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534145796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534145796 none COc1ccc(Sc2nsc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 31, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534145796 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534145796 Building ZINC001534159671 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534159671 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/934 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1) `ZINC001534159671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534159671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534159671 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 6, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 8, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 6, 6, 2, 4, 4, 8, 8, 8, 4, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/935 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1) `ZINC001534159671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534159671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534159671 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 11, 4, 4, 4, 6, 13, 24, 24, 13, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 5, 5, 2, 4, 4, 11, 11, 11, 4, 24, 24, 20, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534159671 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 Building ZINC001534159671 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534159671 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 934) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1) `ZINC001534159671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534159671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534159671 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 6, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 8, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 6, 6, 2, 4, 4, 8, 8, 8, 4, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 935) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1) `ZINC001534159671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534159671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534159671 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 11, 4, 4, 4, 6, 13, 24, 24, 13, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 5, 5, 2, 4, 4, 11, 11, 11, 4, 24, 24, 20, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534159671 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159671 Building ZINC001534159672 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534159672 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/936 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1) `ZINC001534159672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534159672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534159672 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 11, 4, 4, 4, 6, 12, 23, 23, 12, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 5, 5, 2, 4, 4, 11, 11, 11, 4, 23, 23, 19, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/937 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1) `ZINC001534159672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534159672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534159672 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 7, 13, 26, 26, 15, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 5, 5, 2, 4, 4, 8, 8, 8, 4, 26, 26, 21, 26] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534159672 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 Building ZINC001534159672 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534159672 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 936) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1) `ZINC001534159672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534159672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534159672 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 11, 4, 4, 4, 6, 12, 23, 23, 12, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 5, 5, 2, 4, 4, 11, 11, 11, 4, 23, 23, 19, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 937) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1) `ZINC001534159672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534159672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534159672 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)Oc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 7, 13, 26, 26, 15, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 5, 5, 2, 4, 4, 8, 8, 8, 4, 26, 26, 21, 26] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534159672 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534159672 Building ZINC001534162618 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534162618 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/938 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccn2)cc1) `ZINC001534162618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534162618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001534162618 none COc1ccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 50, 49, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 22, 7, 7, 1, 1, 1, 1, 22, 22, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/939 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccn2)cc1) `ZINC001534162618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534162618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001534162618 none COc1ccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 21, 7, 7, 1, 1, 1, 1, 21, 21, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534162618 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 Building ZINC001534162618 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534162618 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 938) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccn2)cc1) `ZINC001534162618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534162618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001534162618 none COc1ccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 50, 49, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 22, 7, 7, 1, 1, 1, 1, 22, 22, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 939) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccn2)cc1) `ZINC001534162618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534162618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001534162618 none COc1ccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)ccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 21, 7, 7, 1, 1, 1, 1, 21, 21, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534162618 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534162618 Building ZINC001534163659 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534163659 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/940 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc(OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001534163659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534163659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001534163659 none CC(C)c1ccc(OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 26, 20, 26, 26, 20, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/941 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc(OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001534163659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534163659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001534163659 none CC(C)c1ccc(OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 28, 23, 28, 28, 23, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5, 28, 28] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534163659 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 Building ZINC001534163659 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534163659 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 940) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc(OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001534163659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534163659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001534163659 none CC(C)c1ccc(OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 26, 20, 26, 26, 20, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 941) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc(OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001534163659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534163659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001534163659 none CC(C)c1ccc(OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 28, 23, 28, 28, 23, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5, 28, 28] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534163659 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534163659 Building ZINC001534179344 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534179344 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/942 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001534179344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534179344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534179344 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 24, 29, 29, 27, 29, 29, 9, 17, 17, 12, 15, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 24, 24, 29, 29, 29, 29, 17, 17, 17, 17, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/943 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001534179344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534179344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534179344 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 23, 28, 28, 28, 28, 28, 9, 17, 17, 13, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 23, 23, 28, 28, 28, 28, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534179344 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 Building ZINC001534179344 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534179344 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 942) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001534179344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534179344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534179344 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 24, 29, 29, 27, 29, 29, 9, 17, 17, 12, 15, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 24, 24, 29, 29, 29, 29, 17, 17, 17, 17, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 943) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001534179344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534179344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534179344 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 23, 28, 28, 28, 28, 28, 9, 17, 17, 13, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 23, 23, 28, 28, 28, 28, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534179344 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534179344 Building ZINC001534191658 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534191658 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/944 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCC2)cc1Cl) `ZINC001534191658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534191658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001534191658 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 10, 14, 16, 16, 15, 15, 16, 16, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 4, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/945 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCC2)cc1Cl) `ZINC001534191658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534191658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001534191658 none COc1ccc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 12, 15, 15, 13, 13, 15, 15, 12, 12, 12, 12, 6, 6, 6, 12, 12, 12, 6, 6, 4, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534191658 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 Building ZINC001534191658 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534191658 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 944) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCC2)cc1Cl) `ZINC001534191658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534191658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001534191658 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 10, 14, 16, 16, 15, 15, 16, 16, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 4, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 945) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCC2)cc1Cl) `ZINC001534191658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534191658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001534191658 none COc1ccc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Br)cc3)CCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 8, 12, 15, 15, 13, 13, 15, 15, 12, 12, 12, 12, 6, 6, 6, 12, 12, 12, 6, 6, 4, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534191658 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534191658 Building ZINC001534193660 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534193660 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/946 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2ccc(Br)cc2CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534193660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534193660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534193660 none C[C@H]1Cc2ccc(Br)cc2CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 2, 15, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 1, 4] 31 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/947 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2ccc(Br)cc2CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534193660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534193660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534193660 none C[C@H]1Cc2ccc(Br)cc2CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 2, 18, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 6] 38 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534193660 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 Building ZINC001534193660 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534193660 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 946) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2ccc(Br)cc2CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534193660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534193660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534193660 none C[C@H]1Cc2ccc(Br)cc2CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 2, 15, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 1, 4] 31 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 947) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2ccc(Br)cc2CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534193660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534193660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534193660 none C[C@H]1Cc2ccc(Br)cc2CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 2, 18, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 6] 38 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534193660 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193660 Building ZINC001534193661 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534193661 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/948 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2ccc(Br)cc2CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534193661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534193661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534193661 none C[C@@H]1Cc2ccc(Br)cc2CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 5] 15 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/949 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2ccc(Br)cc2CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534193661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534193661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534193661 none C[C@@H]1Cc2ccc(Br)cc2CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 4] 14 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534193661 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 Building ZINC001534193661 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534193661 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 948) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2ccc(Br)cc2CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534193661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534193661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534193661 none C[C@@H]1Cc2ccc(Br)cc2CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 5] 15 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 949) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2ccc(Br)cc2CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534193661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534193661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534193661 none C[C@@H]1Cc2ccc(Br)cc2CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 4] 14 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534193661 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534193661 Building ZINC001534235575 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534235575 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/950 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1) `ZINC001534235575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534235575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235575 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 47, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16, 16, 8, 8, 8, 2, 3, 1, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/951 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1) `ZINC001534235575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534235575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235575 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 44, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16, 16, 8, 8, 8, 3, 3, 1, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534235575 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 Building ZINC001534235575 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534235575 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 950) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1) `ZINC001534235575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534235575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235575 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 47, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16, 16, 8, 8, 8, 2, 3, 1, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 951) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1) `ZINC001534235575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534235575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235575 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 44, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16, 16, 8, 8, 8, 3, 3, 1, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534235575 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235575 Building ZINC001534235576 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534235576 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/952 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1) `ZINC001534235576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534235576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235576 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 15, 15, 39, 45, 45, 45, 45, 45, 15, 15, 15, 15, 15, 15, 9, 9, 9, 3, 3, 1, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 15, 15, 15, 15, 15] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/953 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1) `ZINC001534235576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534235576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235576 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 38, 44, 44, 44, 44, 44, 15, 15, 15, 15, 15, 15, 8, 8, 8, 3, 3, 1, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44, 15, 15, 15, 15, 15] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534235576 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 Building ZINC001534235576 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534235576 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 952) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1) `ZINC001534235576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534235576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235576 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 15, 15, 39, 45, 45, 45, 45, 45, 15, 15, 15, 15, 15, 15, 9, 9, 9, 3, 3, 1, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 15, 15, 15, 15, 15] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 953) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1) `ZINC001534235576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534235576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235576 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 38, 44, 44, 44, 44, 44, 15, 15, 15, 15, 15, 15, 8, 8, 8, 3, 3, 1, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44, 15, 15, 15, 15, 15] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534235576 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235576 Building ZINC001534235577 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534235577 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/954 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1) `ZINC001534235577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534235577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235577 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 14, 14, 42, 47, 47, 47, 47, 47, 14, 14, 14, 14, 14, 14, 8, 8, 8, 3, 3, 1, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 14, 14, 14, 14, 14] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/955 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1) `ZINC001534235577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534235577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235577 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 13, 13, 39, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 13, 8, 8, 8, 3, 3, 1, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534235577 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 Building ZINC001534235577 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534235577 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 954) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1) `ZINC001534235577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534235577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235577 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 14, 14, 42, 47, 47, 47, 47, 47, 14, 14, 14, 14, 14, 14, 8, 8, 8, 3, 3, 1, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 14, 14, 14, 14, 14] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 955) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1) `ZINC001534235577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534235577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235577 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 13, 13, 39, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 13, 8, 8, 8, 3, 3, 1, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534235577 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235577 Building ZINC001534235578 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534235578 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/956 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1) `ZINC001534235578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534235578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235578 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 18, 18, 45, 49, 49, 49, 49, 49, 18, 18, 18, 18, 18, 18, 9, 9, 9, 3, 3, 1, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 18, 18] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/957 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1) `ZINC001534235578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534235578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235578 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 1, 3, 3, 3, 7, 15, 15, 46, 49, 49, 49, 49, 49, 15, 15, 15, 15, 15, 15, 7, 7, 7, 2, 3, 1, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 15, 15, 15, 15, 15] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534235578 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 Building ZINC001534235578 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534235578 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 956) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1) `ZINC001534235578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534235578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235578 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 18, 18, 45, 49, 49, 49, 49, 49, 18, 18, 18, 18, 18, 18, 9, 9, 9, 3, 3, 1, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 18, 18] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 957) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1) `ZINC001534235578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534235578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001534235578 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](OC1CCOCC1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 12, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 1, 3, 3, 3, 7, 15, 15, 46, 49, 49, 49, 49, 49, 15, 15, 15, 15, 15, 15, 7, 7, 7, 2, 3, 1, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 15, 15, 15, 15, 15] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534235578 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534235578 Building ZINC001534237715 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534237715 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/958 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cccc(C)c21) `ZINC001534237715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534237715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534237715 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cccc(C)c21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/959 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cccc(C)c21) `ZINC001534237715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534237715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534237715 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cccc(C)c21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 6, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 20, 20, 19, 20, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534237715 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 Building ZINC001534237715 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534237715 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 958) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cccc(C)c21) `ZINC001534237715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534237715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534237715 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cccc(C)c21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 959) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cccc(C)c21) `ZINC001534237715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534237715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534237715 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cccc(C)c21 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 6, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 20, 20, 19, 20, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534237715 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534237715 Building ZINC001534248349 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534248349 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/960 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534248349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534248349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001534248349 none CC(C)Oc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 35, 11, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 4, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/961 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534248349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534248349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001534248349 none CC(C)Oc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 10, 10, 10, 4, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 10, 10, 10, 4, 8, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534248349 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 Building ZINC001534248349 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534248349 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 960) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534248349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534248349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001534248349 none CC(C)Oc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 35, 11, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 4, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 961) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001534248349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534248349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001534248349 none CC(C)Oc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 10, 10, 10, 4, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 10, 10, 10, 4, 8, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534248349 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534248349 Building ZINC001534257605 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534257605 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/962 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCOc2c(Cl)cc(Cl)cc2Cl)cc1Cl) `ZINC001534257605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534257605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001534257605 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCOc2c(Cl)cc(Cl)cc2Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 9, 9, 9, 5, 5, 2, 10, 10, 13, 13, 22, 22, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/963 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCOc2c(Cl)cc(Cl)cc2Cl)cc1Cl) `ZINC001534257605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534257605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001534257605 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCOc2c(Cl)cc(Cl)cc2Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 9, 9, 9, 5, 5, 2, 10, 10, 12, 12, 21, 21, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534257605 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 Building ZINC001534257605 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534257605 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 962) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCOc2c(Cl)cc(Cl)cc2Cl)cc1Cl) `ZINC001534257605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534257605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001534257605 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCOc2c(Cl)cc(Cl)cc2Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 9, 9, 9, 5, 5, 2, 10, 10, 13, 13, 22, 22, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 963) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCOc2c(Cl)cc(Cl)cc2Cl)cc1Cl) `ZINC001534257605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534257605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001534257605 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCOc2c(Cl)cc(Cl)cc2Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 9, 9, 9, 5, 5, 2, 10, 10, 12, 12, 21, 21, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534257605 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534257605 Building ZINC001534261371 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534261371 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/964 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534261371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261371 none CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 40, 40, 28, 18, 28, 13, 8, 13, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 27, 27, 27, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 18, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [25, 54, 55, 17, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 184 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/965 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534261371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261371 none CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 29, 19, 29, 14, 8, 14, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 16, 28, 28, 28, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 8, 8, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 182 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534261371 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 Building ZINC001534261371 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534261371 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 964) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534261371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261371 none CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 40, 40, 28, 18, 28, 13, 8, 13, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 27, 27, 27, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 18, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [25, 54, 55, 17, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 184 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 965) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534261371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261371 none CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 29, 19, 29, 14, 8, 14, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 16, 28, 28, 28, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 8, 8, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 182 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534261371 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261371 Building ZINC001534261372 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534261372 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/966 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534261372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261372 none CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 39, 26, 39, 20, 13, 20, 7, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 20, 28, 28, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 13, 13, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/967 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534261372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261372 none CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 40, 30, 40, 19, 13, 19, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 29, 29, 29, 29, 41, 41, 41, 41, 41, 41, 41, 41, 41, 30, 13, 13, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [25, 54, 55, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534261372 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 Building ZINC001534261372 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534261372 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 966) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534261372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261372 none CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 39, 26, 39, 20, 13, 20, 7, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 20, 28, 28, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 13, 13, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 967) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534261372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261372 none CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 40, 30, 40, 19, 13, 19, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 29, 29, 29, 29, 41, 41, 41, 41, 41, 41, 41, 41, 41, 30, 13, 13, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [25, 54, 55, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534261372 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261372 Building ZINC001534261373 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534261373 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/968 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534261373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261373 none CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 30, 38, 18, 12, 18, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 32, 32, 32, 32, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [25, 54, 55, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/969 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534261373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261373 none CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 27, 39, 20, 13, 20, 7, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 20, 28, 28, 28, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 13, 13, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534261373 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 Building ZINC001534261373 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534261373 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 968) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534261373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261373 none CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 30, 38, 18, 12, 18, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 32, 32, 32, 32, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [25, 54, 55, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 969) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534261373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261373 none CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 27, 39, 20, 13, 20, 7, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 20, 28, 28, 28, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 13, 13, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534261373 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261373 Building ZINC001534261375 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534261375 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/970 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534261375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261375 none CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 30, 19, 30, 14, 9, 14, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 18, 33, 33, 33, 33, 35, 35, 35, 35, 35, 35, 35, 35, 35, 19, 9, 9, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/971 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534261375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261375 none CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 35, 25, 35, 17, 11, 17, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 31, 31, 31, 31, 42, 42, 42, 42, 42, 42, 42, 42, 42, 25, 11, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [25, 54, 55, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 198 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534261375 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 Building ZINC001534261375 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534261375 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 970) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534261375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261375 none CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 30, 19, 30, 14, 9, 14, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 18, 33, 33, 33, 33, 35, 35, 35, 35, 35, 35, 35, 35, 35, 19, 9, 9, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 971) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1) `ZINC001534261375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534261375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001534261375 none CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 35, 25, 35, 17, 11, 17, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 31, 31, 31, 31, 42, 42, 42, 42, 42, 42, 42, 42, 42, 25, 11, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [25, 54, 55, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 198 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534261375 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534261375 Building ZINC001534316101 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534316101 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/972 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)sc1Cc1ccc(C)cc1) `ZINC001534316101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534316101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001534316101 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)sc1Cc1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 18, 31, 31, 22, 22, 31, 31, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 18, 18, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/973 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)sc1Cc1ccc(C)cc1) `ZINC001534316101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534316101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001534316101 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)sc1Cc1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 18, 31, 31, 22, 24, 31, 31, 4, 4, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 18, 18, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534316101 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 Building ZINC001534316101 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534316101 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 972) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)sc1Cc1ccc(C)cc1) `ZINC001534316101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534316101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001534316101 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)sc1Cc1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 18, 31, 31, 22, 22, 31, 31, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 18, 18, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 973) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)sc1Cc1ccc(C)cc1) `ZINC001534316101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534316101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001534316101 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)sc1Cc1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 18, 31, 31, 22, 24, 31, 31, 4, 4, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 18, 18, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534316101 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316101 Building ZINC001534316296 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534316296 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/974 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(C)cc1) `ZINC001534316296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534316296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001534316296 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 21, 29, 29, 25, 25, 29, 29, 5, 5, 5, 3, 7, 7, 21, 21, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/975 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(C)cc1) `ZINC001534316296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534316296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001534316296 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 21, 29, 29, 25, 29, 29, 29, 5, 5, 5, 3, 7, 7, 21, 21, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534316296 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 Building ZINC001534316296 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534316296 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 974) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(C)cc1) `ZINC001534316296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534316296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001534316296 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 21, 29, 29, 25, 25, 29, 29, 5, 5, 5, 3, 7, 7, 21, 21, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 975) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(C)cc1) `ZINC001534316296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534316296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001534316296 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)sc1Cc1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 21, 29, 29, 25, 29, 29, 29, 5, 5, 5, 3, 7, 7, 21, 21, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534316296 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534316296 Building ZINC001534329559 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534329559 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/976 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)sc1Cc1cccc(Br)c1) `ZINC001534329559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534329559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001534329559 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)sc1Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 3, 3, 10, 27, 27, 27, 27, 27, 27, 3, 3, 3, 2, 3, 3, 2, 3, 3, 3, 3, 10, 10, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/977 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)sc1Cc1cccc(Br)c1) `ZINC001534329559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534329559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001534329559 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)sc1Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 28, 28, 20, 28, 28, 28, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 11, 11, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534329559 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 Building ZINC001534329559 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534329559 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 976) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)sc1Cc1cccc(Br)c1) `ZINC001534329559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534329559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001534329559 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)sc1Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 3, 3, 10, 27, 27, 27, 27, 27, 27, 3, 3, 3, 2, 3, 3, 2, 3, 3, 3, 3, 10, 10, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 977) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)sc1Cc1cccc(Br)c1) `ZINC001534329559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534329559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001534329559 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)sc1Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 28, 28, 20, 28, 28, 28, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 11, 11, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534329559 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534329559 Building ZINC001534360305 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534360305 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/978 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccsc1)c1ccc(Br)cc1) `ZINC001534360305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534360305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534360305 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccsc1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 9, 18, 38, 38, 38, 38, 9, 18, 18, 12, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 38, 38, 38, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/979 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccsc1)c1ccc(Br)cc1) `ZINC001534360305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534360305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534360305 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccsc1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 8, 19, 38, 38, 38, 38, 8, 15, 15, 8, 8, 15, 15, 4, 4, 4, 4, 4, 4, 4, 19, 19, 38, 38, 38, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534360305 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 Building ZINC001534360305 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534360305 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 978) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccsc1)c1ccc(Br)cc1) `ZINC001534360305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534360305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534360305 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccsc1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 9, 18, 38, 38, 38, 38, 9, 18, 18, 12, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 38, 38, 38, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 979) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccsc1)c1ccc(Br)cc1) `ZINC001534360305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534360305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534360305 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccsc1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 14, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 8, 19, 38, 38, 38, 38, 8, 15, 15, 8, 8, 15, 15, 4, 4, 4, 4, 4, 4, 4, 19, 19, 38, 38, 38, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534360305 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534360305 Building ZINC001534364155 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534364155 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/980 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/980' -> `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)Nc1ccc(Oc2cc(F)cc(F)c2)nc1) `ZINC001534364155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534364155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001534364155 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cc(F)cc(F)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 26, 39, 39, 39, 26, 39, 39, 39, 8, 8, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 8, 8, 39, 33, 39, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/981 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/981' -> `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)Nc1ccc(Oc2cc(F)cc(F)c2)nc1) `ZINC001534364155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534364155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001534364155 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cc(F)cc(F)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 26, 40, 40, 40, 29, 40, 40, 40, 8, 8, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 8, 8, 40, 33, 40, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534364155 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 Building ZINC001534364155 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534364155 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 980) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccc(Oc2cc(F)cc(F)c2)nc1) `ZINC001534364155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534364155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001534364155 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cc(F)cc(F)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 26, 39, 39, 39, 26, 39, 39, 39, 8, 8, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 8, 8, 39, 33, 39, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 981) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1ccc(Oc2cc(F)cc(F)c2)nc1) `ZINC001534364155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534364155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001534364155 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cc(F)cc(F)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 26, 40, 40, 40, 29, 40, 40, 40, 8, 8, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 8, 8, 40, 33, 40, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/150923/xbj-8058088.36/working/building/ZINC001534364155 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534364155 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534364155 Building ZINC001534393009 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534393009 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/982 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1) `ZINC001534393009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534393009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001534393009 none CCOc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 5, 4, 11, 11, 4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 4, 14, 14, 10, 14, 14, 14, 11, 11, 18, 18, 18, 18, 18, 11, 11, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 14, 14, 14, 14, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/983 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1) `ZINC001534393009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534393009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001534393009 none CCOc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 4, 4, 13, 13, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 4, 14, 14, 12, 14, 14, 14, 13, 13, 20, 20, 20, 20, 20, 13, 13, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534393009 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 Building ZINC001534393009 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534393009 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 982) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1) `ZINC001534393009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534393009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001534393009 none CCOc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 5, 4, 11, 11, 4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 4, 14, 14, 10, 14, 14, 14, 11, 11, 18, 18, 18, 18, 18, 11, 11, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 14, 14, 14, 14, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 983) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1) `ZINC001534393009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534393009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001534393009 none CCOc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 4, 4, 13, 13, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 4, 14, 14, 12, 14, 14, 14, 13, 13, 20, 20, 20, 20, 20, 13, 13, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 14, 14, 14, 14, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534393009 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393009 Building ZINC001534393011 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534393011 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/984 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1) `ZINC001534393011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534393011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001534393011 none CCOc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 13, 13, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 4, 13, 13, 10, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 13, 13, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/985 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1) `ZINC001534393011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534393011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001534393011 none CCOc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 6, 4, 11, 11, 4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 4, 13, 13, 12, 13, 13, 13, 11, 11, 19, 19, 19, 19, 19, 11, 11, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 13, 13, 13, 13, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534393011 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 Building ZINC001534393011 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534393011 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 984) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1) `ZINC001534393011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534393011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001534393011 none CCOc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 13, 13, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 4, 13, 13, 10, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 13, 13, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 985) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1) `ZINC001534393011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534393011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001534393011 none CCOc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 6, 4, 11, 11, 4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 4, 13, 13, 12, 13, 13, 13, 11, 11, 19, 19, 19, 19, 19, 11, 11, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 13, 13, 13, 13, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534393011 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534393011 Building ZINC001534395993 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534395993 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/986 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CCCC2)cc1) `ZINC001534395993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534395993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001534395993 none CC(C)(C)c1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 36, 36, 23, 23, 23, 21, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 23, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/987 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CCCC2)cc1) `ZINC001534395993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534395993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001534395993 none CC(C)(C)c1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 36, 36, 24, 24, 24, 24, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 24, 10, 10, 2, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534395993 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 Building ZINC001534395993 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534395993 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 986) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CCCC2)cc1) `ZINC001534395993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534395993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001534395993 none CC(C)(C)c1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 36, 36, 23, 23, 23, 21, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 23, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 987) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CCCC2)cc1) `ZINC001534395993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534395993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001534395993 none CC(C)(C)c1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 36, 36, 24, 24, 24, 24, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 24, 10, 10, 2, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534395993 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534395993 Building ZINC001534422205 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534422205 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/988 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc(Br)cc1F) `ZINC001534422205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534422205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534422205 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 12, 12, 23, 23, 19, 23, 23, 12, 35, 35, 12, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 5, 6, 23, 23, 23, 23, 23, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/989 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc(Br)cc1F) `ZINC001534422205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534422205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534422205 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 12, 12, 24, 24, 12, 24, 24, 12, 35, 35, 14, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 5, 6, 24, 24, 24, 24, 24, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534422205 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 Building ZINC001534422205 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534422205 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 988) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc(Br)cc1F) `ZINC001534422205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534422205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534422205 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 12, 12, 23, 23, 19, 23, 23, 12, 35, 35, 12, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 5, 6, 23, 23, 23, 23, 23, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 989) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc(Br)cc1F) `ZINC001534422205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534422205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534422205 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 12, 12, 24, 24, 12, 24, 24, 12, 35, 35, 14, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 5, 6, 24, 24, 24, 24, 24, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534422205 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422205 Building ZINC001534422206 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534422206 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/990 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc(Br)cc1F) `ZINC001534422206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534422206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534422206 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 12, 12, 24, 24, 14, 24, 24, 12, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 5, 6, 24, 24, 14, 24, 24, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/991 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc(Br)cc1F) `ZINC001534422206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534422206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534422206 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 12, 12, 23, 23, 14, 23, 23, 12, 34, 34, 17, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 6, 23, 23, 14, 23, 23, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534422206 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 Building ZINC001534422206 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534422206 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 990) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc(Br)cc1F) `ZINC001534422206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534422206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534422206 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 12, 12, 24, 24, 14, 24, 24, 12, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 5, 6, 24, 24, 14, 24, 24, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 991) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc(Br)cc1F) `ZINC001534422206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534422206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001534422206 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 12, 12, 23, 23, 14, 23, 23, 12, 34, 34, 17, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 6, 23, 23, 14, 23, 23, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534422206 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534422206 Building ZINC001534434113 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534434113 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/992 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1C) `ZINC001534434113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534434113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534434113 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 7, 11, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/993 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1C) `ZINC001534434113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534434113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534434113 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 64 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534434113 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 Building ZINC001534434113 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534434113 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 992) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1C) `ZINC001534434113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534434113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534434113 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 7, 11, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 77 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 993) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1C) `ZINC001534434113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534434113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001534434113 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 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: 64 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534434113 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534434113 Building ZINC001534457922 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534457922 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/994 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534457922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534457922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534457922 none C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 23, 42, 42, 42, 42, 42, 42, 42, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 23, 23, 42, 42, 42, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/995 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534457922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534457922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534457922 none C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 25, 44, 44, 44, 44, 44, 44, 44, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 25, 25, 44, 44, 44, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534457922 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 Building ZINC001534457922 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534457922 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 994) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534457922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534457922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534457922 none C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 23, 42, 42, 42, 42, 42, 42, 42, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 23, 23, 42, 42, 42, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 995) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534457922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534457922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534457922 none C[C@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 25, 44, 44, 44, 44, 44, 44, 44, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 25, 25, 44, 44, 44, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534457922 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457922 Building ZINC001534457927 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534457927 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/996 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534457927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534457927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534457927 none C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 25, 44, 44, 44, 44, 44, 44, 44, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 25, 25, 44, 44, 44, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/997 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534457927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534457927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534457927 none C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 23, 42, 42, 42, 42, 42, 42, 42, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 23, 23, 42, 42, 42, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534457927 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 Building ZINC001534457927 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534457927 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 996) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534457927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534457927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534457927 none C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 25, 44, 44, 44, 44, 44, 44, 44, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 25, 25, 44, 44, 44, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 997) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534457927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534457927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001534457927 none C[C@@H](Cc1ccc(F)c(Br)c1)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 23, 42, 42, 42, 42, 42, 42, 42, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 23, 23, 42, 42, 42, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534457927 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534457927 Building ZINC001534478731 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534478731 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/998 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccn1) `ZINC001534478731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534478731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001534478731 none CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 3, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 5, 5, 5, 5, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/999 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccn1) `ZINC001534478731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534478731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001534478731 none CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534478731 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 Building ZINC001534478731 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001534478731 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 998) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccn1) `ZINC001534478731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534478731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001534478731 none CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 3, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 5, 5, 5, 5, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 mkdir: created directory `1' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/1 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 1 (index: 999) grep: /scratch/xiaobo/150923/xbj-8058088.36/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccn1) `ZINC001534478731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001534478731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001534478731 none CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534478731 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/0.* 1: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731/1.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534478731 Building ZINC001534503401 mkdir: created directory `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534503401' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534503401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001534503401 mkdir: created directory `0' /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534503401/0 /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534503401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/150923/xbj-8058088.36/working/3D/1000 `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccn2)nc2sccc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001534503401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001534503401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534503401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001534503401 none O=C(Nc1nc(c2ccccn2)nc2sccc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 14, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 20, 20, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 42, 42, 42, 42, 20, 20, 4, 2, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534503401 /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Finished preparing ZINC001534503401 Recording results /scratch/xiaobo/150923/xbj-8058088.36/working /scratch/xiaobo/150923/xbj-8058088.36 Appending to /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.* 0: /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534503401/0.* Removing working files in /scratch/xiaobo/150923/xbj-8058088.36/working/building/ZINC001534503401 /scratch/xiaobo/150923/xbj-8058088.36 Compressing combined databse files /scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/150923/xbj-8058088.36/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/395' removed `/scratch/xiaobo/150923/xbj-8058088.36/working/3D/1001' removed directory: `/scratch/xiaobo/150923/xbj-8058088.36/working/3D' `/scratch/xiaobo/150923/xbj-8058088.36/working/protonate' -> `/scratch/xiaobo/150923/xbj-8058088.36/archive' `/scratch/xiaobo/150923/xbj-8058088.36/working/input-smiles.ism' -> `/scratch/xiaobo/150923/xbj-8058088.36/archive/input-smiles.ism' rmdir: removing directory, `/scratch/xiaobo/150923/xbj-8058088.36/working/building' rmdir: removing directory, `/scratch/xiaobo/150923/xbj-8058088.36/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/150923/xbj-8058088.36' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj' `/scratch/xiaobo/150923/xbj-8058088.36/archive' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/archive' `/scratch/xiaobo/150923/xbj-8058088.36/archive/xbj-protonated-manual.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/archive/xbj-protonated-manual.ism' `/scratch/xiaobo/150923/xbj-8058088.36/archive/xbj-protomers-expanded.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/archive/xbj-protomers-expanded.ism' `/scratch/xiaobo/150923/xbj-8058088.36/archive/xbj-protomers.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/archive/xbj-protomers.ism' `/scratch/xiaobo/150923/xbj-8058088.36/archive/input-smiles.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/archive/input-smiles.ism' `/scratch/xiaobo/150923/xbj-8058088.36/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/finished' `/scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/finished/xbj.db2.gz' `/scratch/xiaobo/150923/xbj-8058088.36/failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/failure-reason' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/failure-reason' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/ZINC001528684114.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/ZINC001528684114.ism' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/ZINC001528684114-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/ZINC001528684114-numbered.ism' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/input.ism' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.12' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/failure-reason' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/outputwat.log' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.o-wat' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/0.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/0.mol2' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.20' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/name.txt' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/ZINC001528684114.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/ZINC001528684114.mol2' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.in-hex' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/outputhex.log' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.ZmatMOPAC' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.21' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.in-wat' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.mol2' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/temp.o-hex' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.19' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114.ism' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/ZINC001528684114-numbered.ism' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/input.ism' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/fort.12' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/failure-reason' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/outputwat.log' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/temp.o-wat' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/0.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/0.mol2' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/fort.20' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/name.txt' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/ZINC001528684114.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/ZINC001528684114.mol2' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/temp.in-hex' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/outputhex.log' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/temp.ZmatMOPAC' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/fort.21' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/temp.in-wat' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/temp.mol2' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/temp.o-hex' `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/0.failed/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbj/failed/ZINC001528684114/0.failed/fort.19' removed `/scratch/xiaobo/150923/xbj-8058088.36/archive/xbj-protonated-manual.ism' removed `/scratch/xiaobo/150923/xbj-8058088.36/archive/xbj-protomers-expanded.ism' removed `/scratch/xiaobo/150923/xbj-8058088.36/archive/xbj-protomers.ism' removed `/scratch/xiaobo/150923/xbj-8058088.36/archive/input-smiles.ism' removed directory: `/scratch/xiaobo/150923/xbj-8058088.36/archive' removed `/scratch/xiaobo/150923/xbj-8058088.36/finished/xbj.db2.gz' removed directory: `/scratch/xiaobo/150923/xbj-8058088.36/finished' removed `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/failure-reason' removed `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/failure-reason' removed `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/ZINC001528684114.ism' removed `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/ZINC001528684114-numbered.ism' removed `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/input.ism' removed `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/fort.12' removed `/scratch/xiaobo/150923/xbj-8058088.36/failed/ZINC001528684114/ZINC001528684114/0.failed/failure-reason' removed 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